Mercurial > repos > chemteam > acpype_amber2gromacs

comparison macros.xml @ 1:5b4ae74b7f0b draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
author chemteam
date Thu, 27 Jan 2022 17:19:05 +0000
parents 79c856227ff1
children
comparison
equal deleted inserted replaced
0:79c856227ff1 1:5b4ae74b7f0b
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">21.10</token> 2 <token name="@TOOL_VERSION@">21.10</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">ambertools</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">ambertools</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 <xml name="citations"> 9 <xml name="builtin_amberfiles">
10 <citations> 10 <param name="arg_filename" type="select" label="File">
11 <citation type="doi">10.1002/jcc.20290</citation> 11 <option value="epASN.prepin">epASN.prepin</option>
12 <citation type="bibtex"> 12 <option value="epACE.prepin">epACE.prepin</option>
13 <option value="GLYCAM_06j-1.prep">GLYCAM_06j-1.prep</option>
14 <option value="toyrna.in">toyrna.in</option>
15 <option value="epTRP.prepin">epTRP.prepin</option>
16 <option value="epSER.prepin">epSER.prepin</option>
17 <option value="epALA.prepin">epALA.prepin</option>
18 <option value="epASP.prepin">epASP.prepin</option>
19 <option value="amino12.in">amino12.in</option>
20 <option value="amino10.in">amino10.in</option>
21 <option value="epPHE.prepin">epPHE.prepin</option>
22 <option value="uni_amino03.in">uni_amino03.in</option>
23 <option value="aminoct12.in">aminoct12.in</option>
24 <option value="epTHR.prepin">epTHR.prepin</option>
25 <option value="uni_aminoct03.in">uni_aminoct03.in</option>
26 <option value="epNME.prepin">epNME.prepin</option>
27 <option value="chcl3.in">chcl3.in</option>
28 <option value="all_aminont03.in">all_aminont03.in</option>
29 <option value="epTYR.prepin">epTYR.prepin</option>
30 <option value="epVAL.prepin">epVAL.prepin</option>
31 <option value="epGLU.prepin">epGLU.prepin</option>
32 <option value="meoh.in">meoh.in</option>
33 <option value="all_aminoct03.in">all_aminoct03.in</option>
34 <option value="epHID.prepin">epHID.prepin</option>
35 <option value="all_amino03.in">all_amino03.in</option>
36 <option value="aminont10.in">aminont10.in</option>
37 <option value="epLEU.prepin">epLEU.prepin</option>
38 <option value="GLYCAM_lipids_06h.prep">GLYCAM_lipids_06h.prep</option>
39 <option value="GLYCAM_06EPb.prep">GLYCAM_06EPb.prep</option>
40 <option value="epILE.prepin">epILE.prepin</option>
41 <option value="epHIE.prepin">epHIE.prepin</option>
42 <option value="aminoct10.in">aminoct10.in</option>
43 <option value="epCYS.prepin">epCYS.prepin</option>
44 <option value="epGLN.prepin">epGLN.prepin</option>
45 <option value="epLYS.prepin">epLYS.prepin</option>
46 <option value="epARG.prepin">epARG.prepin</option>
47 <option value="epGLY.prepin">epGLY.prepin</option>
48 <option value="nma.in">nma.in</option>
49 <option value="uni_aminont03.in">uni_aminont03.in</option>
50 <option value="nucleic10.in">nucleic10.in</option>
51 <option value="epMET.prepin">epMET.prepin</option>
52 <option value="dna_nuc94-bsc0_chiOl4-ezOL1.in">dna_nuc94-bsc0_chiOl4-ezOL1.in</option>
53 <option value="aminont12.in">aminont12.in</option>
54 <option value="protonated_nucleic/RGE_noP.pdb">protonated_nucleic/RGE_noP.pdb</option>
55 <option value="protonated_nucleic/DA+_noP.pdb">protonated_nucleic/DA+_noP.pdb</option>
56 <option value="protonated_nucleic/DC+.pdb">protonated_nucleic/DC+.pdb</option>
57 <option value="protonated_nucleic/RC+_noP.pdb">protonated_nucleic/RC+_noP.pdb</option>
58 <option value="protonated_nucleic/DC+_noP.pdb">protonated_nucleic/DC+_noP.pdb</option>
59 <option value="protonated_nucleic/RC+.pdb">protonated_nucleic/RC+.pdb</option>
60 <option value="protonated_nucleic/RGE.pdb">protonated_nucleic/RGE.pdb</option>
61 <option value="protonated_nucleic/DTE_noP.pdb">protonated_nucleic/DTE_noP.pdb</option>
62 <option value="protonated_nucleic/DGE_noP.pdb">protonated_nucleic/DGE_noP.pdb</option>
63 <option value="protonated_nucleic/RG-.pdb">protonated_nucleic/RG-.pdb</option>
64 <option value="protonated_nucleic/RU-_noP.pdb">protonated_nucleic/RU-_noP.pdb</option>
65 <option value="protonated_nucleic/DT-_noP.pdb">protonated_nucleic/DT-_noP.pdb</option>
66 <option value="protonated_nucleic/RA+_noP.pdb">protonated_nucleic/RA+_noP.pdb</option>
67 <option value="protonated_nucleic/DA+.pdb">protonated_nucleic/DA+.pdb</option>
68 <option value="protonated_nucleic/RUE_noP.pdb">protonated_nucleic/RUE_noP.pdb</option>
69 <option value="protonated_nucleic/DTE.pdb">protonated_nucleic/DTE.pdb</option>
70 <option value="protonated_nucleic/DT-.pdb">protonated_nucleic/DT-.pdb</option>
71 <option value="protonated_nucleic/DG-.pdb">protonated_nucleic/DG-.pdb</option>
72 <option value="protonated_nucleic/RG-_noP.pdb">protonated_nucleic/RG-_noP.pdb</option>
73 <option value="protonated_nucleic/DG-_noP.pdb">protonated_nucleic/DG-_noP.pdb</option>
74 <option value="protonated_nucleic/DGE.pdb">protonated_nucleic/DGE.pdb</option>
75 <option value="protonated_nucleic/RU-.pdb">protonated_nucleic/RU-.pdb</option>
76 <option value="protonated_nucleic/RA+.pdb">protonated_nucleic/RA+.pdb</option>
77 <option value="protonated_nucleic/RUE.pdb">protonated_nucleic/RUE.pdb</option>
78 <option value="oldff/all_amino02.r1.in">oldff/all_amino02.r1.in</option>
79 <option value="oldff/all.in">oldff/all.in</option>
80 <option value="oldff/all_amino02.in">oldff/all_amino02.in</option>
81 <option value="oldff/opls_unict.in">oldff/opls_unict.in</option>
82 <option value="oldff/unint.in">oldff/unint.in</option>
83 <option value="oldff/all_aminoct94.in">oldff/all_aminoct94.in</option>
84 <option value="oldff/protein.amberua.in">oldff/protein.amberua.in</option>
85 <option value="oldff/protein.amberua.N.in">oldff/protein.amberua.N.in</option>
86 <option value="oldff/all_amino02EP.in">oldff/all_amino02EP.in</option>
87 <option value="oldff/all_aminont02EP.in">oldff/all_aminont02EP.in</option>
88 <option value="oldff/GLYCAM_06j.prep">oldff/GLYCAM_06j.prep</option>
89 <option value="oldff/opls_uni.in">oldff/opls_uni.in</option>
90 <option value="oldff/protein.amberua.C.in">oldff/protein.amberua.C.in</option>
91 <option value="oldff/all_nuc02.in">oldff/all_nuc02.in</option>
92 <option value="oldff/all_nuc94.in">oldff/all_nuc94.in</option>
93 <option value="oldff/all_amino94.in">oldff/all_amino94.in</option>
94 <option value="oldff/GLYCAM_06h.prep">oldff/GLYCAM_06h.prep</option>
95 <option value="oldff/opls_nacl.in">oldff/opls_nacl.in</option>
96 <option value="oldff/all_aminont94.in">oldff/all_aminont94.in</option>
97 <option value="oldff/allnt.in">oldff/allnt.in</option>
98 <option value="oldff/all_aminoct02EP.in">oldff/all_aminoct02EP.in</option>
99 <option value="oldff/all_aminoct02.in">oldff/all_aminoct02.in</option>
100 <option value="oldff/unict.in">oldff/unict.in</option>
101 <option value="oldff/allct.in">oldff/allct.in</option>
102 <option value="oldff/all_nuc02EP.in">oldff/all_nuc02EP.in</option>
103 <option value="oldff/opls_unint.in">oldff/opls_unint.in</option>
104 <option value="oldff/all_aminont02.in">oldff/all_aminont02.in</option>
105 <option value="oldff/na.amberua.in">oldff/na.amberua.in</option>
106 <option value="oldff/uni.in">oldff/uni.in</option>
107 <option value="nucleic12.redq.lib">nucleic12.redq.lib</option>
108 <option value="all_aminontfb15.lib">all_aminontfb15.lib</option>
109 <option value="ff03ua.cmd">ff03ua.cmd</option>
110 <option value="ff94.log">ff94.log</option>
111 <option value="amino19ipq_0.9_vac.lib">amino19ipq_0.9_vac.lib</option>
112 <option value="fb4box.off">fb4box.off</option>
113 <option value="aminont10.lib">aminont10.lib</option>
114 <option value="all_aminont03.lib">all_aminont03.lib</option>
115 <option value="tip4pbox.off">tip4pbox.off</option>
116 <option value="atomic_ions.cmd">atomic_ions.cmd</option>
117 <option value="8Mureabox.off">8Mureabox.off</option>
118 <option value="parmBSC1.lib">parmBSC1.lib</option>
119 <option value="GLYCAM_amino_06j_12SB.lib">GLYCAM_amino_06j_12SB.lib</option>
120 <option value="all_aminofb15.lib">all_aminofb15.lib</option>
121 <option value="amino14ipq.lib">amino14ipq.lib</option>
122 <option value="ff03.log">ff03.log</option>
123 <option value="aminoct19ipq_0.9.lib">aminoct19ipq_0.9.lib</option>
124 <option value="aminont19ipq_0.9_pol.lib">aminont19ipq_0.9_pol.lib</option>
125 <option value="all_aminont94.lib">all_aminont94.lib</option>
126 <option value="DNA_CI.lib">DNA_CI.lib</option>
127 <option value="all_nucleic94.lib">all_nucleic94.lib</option>
128 <option value="GLYCAM_aminont_06j_12SB.lib">GLYCAM_aminont_06j_12SB.lib</option>
129 <option value="atomic_ions.log">atomic_ions.log</option>
130 <option value="amino19ipq_0.9_pol.lib">amino19ipq_0.9_pol.lib</option>
131 <option value="amino19ipq_0.9.lib">amino19ipq_0.9.lib</option>
132 <option value="phos_amino94.lib">phos_amino94.lib</option>
133 <option value="tip4pewbox.off">tip4pewbox.off</option>
134 <option value="tip4pd.off">tip4pd.off</option>
135 <option value="mod_amino.lib">mod_amino.lib</option>
136 <option value="conste.lib">conste.lib</option>
137 <option value="nucleic10.lib">nucleic10.lib</option>
138 <option value="chcl3box.off">chcl3box.off</option>
139 <option value="aminont12.redq.lib">aminont12.redq.lib</option>
140 <option value="all_aminoct94.lib">all_aminoct94.lib</option>
141 <option value="amino15ipq-vac_10.0.lib">amino15ipq-vac_10.0.lib</option>
142 <option value="residues.RNA.parmCHI_YIL.bsc.lib">residues.RNA.parmCHI_YIL.bsc.lib</option>
143 <option value="tip3pbox.off">tip3pbox.off</option>
144 <option value="solvents.lib">solvents.lib</option>
145 <option value="aminoct12.redq.lib">aminoct12.redq.lib</option>
146 <option value="tip3pfbox.off">tip3pfbox.off</option>
147 <option value="DNA.OL15.lib">DNA.OL15.lib</option>
148 <option value="ff10.cmd">ff10.cmd</option>
149 <option value="aminoct12.lib">aminoct12.lib</option>
150 <option value="aminoct19ipq_0.9_pol.lib">aminoct19ipq_0.9_pol.lib</option>
151 <option value="tip5pbox.off">tip5pbox.off</option>
152 <option value="all_amino03.lib">all_amino03.lib</option>
153 <option value="atomic_ions.lib">atomic_ions.lib</option>
154 <option value="8Murea.readme">8Murea.readme</option>
155 <option value="ff03ua.log">ff03ua.log</option>
156 <option value="all_amino94.lib">all_amino94.lib</option>
157 <option value="uni_aminont03.lib">uni_aminont03.lib</option>
158 <option value="nucleic12.LJbb-RNA.lib">nucleic12.LJbb-RNA.lib</option>
159 <option value="nmabox.off">nmabox.off</option>
160 <option value="RNA.YIL.lib">RNA.YIL.lib</option>
161 <option value="xFPchromophores.lib">xFPchromophores.lib</option>
162 <option value="ff94.cmd">ff94.cmd</option>
163 <option value="nab.lib">nab.lib</option>
164 <option value="terminalphos.LJbb-RNA.lib">terminalphos.LJbb-RNA.lib</option>
165 <option value="opcbox.off">opcbox.off</option>
166 <option value="ff03.cmd">ff03.cmd</option>
167 <option value="music.lib">music.lib</option>
168 <option value="all_prot_nucleic10.lib">all_prot_nucleic10.lib</option>
169 <option value="aminoct19ipq_0.9_vac.lib">aminoct19ipq_0.9_vac.lib</option>
170 <option value="all_aminoAM1.lib">all_aminoAM1.lib</option>
171 <option value="all_amino94ildn.lib">all_amino94ildn.lib</option>
172 <option value="ions94.lib">ions94.lib</option>
173 <option value="all_aminoct03.lib">all_aminoct03.lib</option>
174 <option value="RNA.lib">RNA.lib</option>
175 <option value="spcebox.off">spcebox.off</option>
176 <option value="aminont19ipq_0.9_vac.lib">aminont19ipq_0.9_vac.lib</option>
177 <option value="nucleic12.lib">nucleic12.lib</option>
178 <option value="lipid17.lib">lipid17.lib</option>
179 <option value="terminal_monophosphate.lib">terminal_monophosphate.lib</option>
180 <option value="all_prot_nucleic10.log">all_prot_nucleic10.log</option>
181 <option value="ions94.cmd">ions94.cmd</option>
182 <option value="aminont15ipq_10.0.lib">aminont15ipq_10.0.lib</option>
183 <option value="aminocn15ipq_10.0.lib">aminocn15ipq_10.0.lib</option>
184 <option value="mk_nablib.cmd">mk_nablib.cmd</option>
185 <option value="all_modrna08.lib">all_modrna08.lib</option>
186 <option value="aminont12.lib">aminont12.lib</option>
187 <option value="pol3box.off">pol3box.off</option>
188 <option value="ff15ipq-m.lib">ff15ipq-m.lib</option>
189 <option value="phmd.lib">phmd.lib</option>
190 <option value="RNA_CI.lib">RNA_CI.lib</option>
191 <option value="solvents.log">solvents.log</option>
192 <option value="GLYCAM_aminoct_06j_12SB.lib">GLYCAM_aminoct_06j_12SB.lib</option>
193 <option value="amberdyes.lib">amberdyes.lib</option>
194 <option value="uni_aminoct03.lib">uni_aminoct03.lib</option>
195 <option value="phosaa14SB.lib">phosaa14SB.lib</option>
196 <option value="all_aminoPM3.lib">all_aminoPM3.lib</option>
197 <option value="meohbox.off">meohbox.off</option>
198 <option value="amino19.lib">amino19.lib</option>
199 <option value="fb3box.off">fb3box.off</option>
200 <option value="ff12SB.log">ff12SB.log</option>
201 <option value="Makefile">Makefile</option>
202 <option value="aminont14ipq.lib">aminont14ipq.lib</option>
203 <option value="aminoct10.lib">aminoct10.lib</option>
204 <option value="RNA_Shaw.lib">RNA_Shaw.lib</option>
205 <option value="mk_nablib.log">mk_nablib.log</option>
206 <option value="ff10.log">ff10.log</option>
207 <option value="constph.lib">constph.lib</option>
208 <option value="all_nucleic94.nmr.lib">all_nucleic94.nmr.lib</option>
209 <option value="mod_amino19.lib">mod_amino19.lib</option>
210 <option value="ions94.log">ions94.log</option>
211 <option value="aminoct15ipq_10.0.lib">aminoct15ipq_10.0.lib</option>
212 <option value="ff12SB.cmd">ff12SB.cmd</option>
213 <option value="nucleic12.ROC-RNA.lib">nucleic12.ROC-RNA.lib</option>
214 <option value="lipid14.lib">lipid14.lib</option>
215 <option value="amino10.lib">amino10.lib</option>
216 <option value="amino15ipq_10.0.lib">amino15ipq_10.0.lib</option>
217 <option value="all_aminont94ildn.lib">all_aminont94ildn.lib</option>
218 <option value="all_aminoctfb15.lib">all_aminoctfb15.lib</option>
219 <option value="parmBSC0.lib">parmBSC0.lib</option>
220 <option value="solvents.cmd">solvents.cmd</option>
221 <option value="spcfwbox.off">spcfwbox.off</option>
222 <option value="cph_nucleic_caps.lib">cph_nucleic_caps.lib</option>
223 <option value="opc3box.off">opc3box.off</option>
224 <option value="amino12.redq.lib">amino12.redq.lib</option>
225 <option value="aminont15ipq-vac_10.0.lib">aminont15ipq-vac_10.0.lib</option>
226 <option value="all_prot_nucleic10.cmd">all_prot_nucleic10.cmd</option>
227 <option value="phosaa19SB.lib">phosaa19SB.lib</option>
228 <option value="qspcfwbox.off">qspcfwbox.off</option>
229 <option value="uni_amino03.lib">uni_amino03.lib</option>
230 <option value="all_amino94.nmr.lib">all_amino94.nmr.lib</option>
231 <option value="aminoct14ipq.lib">aminoct14ipq.lib</option>
232 <option value="aminont19ipq_0.9.lib">aminont19ipq_0.9.lib</option>
233 <option value="aminoct15ipq-vac_10.0.lib">aminoct15ipq-vac_10.0.lib</option>
234 <option value="all_aminoct94ildn.lib">all_aminoct94ildn.lib</option>
235 <option value="amino12.lib">amino12.lib</option>
236 <option value="oldff/ff02.log">oldff/ff02.log</option>
237 <option value="oldff/phosphoaa10.lib">oldff/phosphoaa10.lib</option>
238 <option value="oldff/all_nucleic91.lib">oldff/all_nucleic91.lib</option>
239 <option value="oldff/all_aminoct02.lib">oldff/all_aminoct02.lib</option>
240 <option value="oldff/ff02.cmd">oldff/ff02.cmd</option>
241 <option value="oldff/all_nucleic02EP.lib">oldff/all_nucleic02EP.lib</option>
242 <option value="oldff/ions91.lib">oldff/ions91.lib</option>
243 <option value="oldff/dna.amberua.lib">oldff/dna.amberua.lib</option>
244 <option value="oldff/all_aminoct91.lib">oldff/all_aminoct91.lib</option>
245 <option value="oldff/all_aminoct02EP.lib">oldff/all_aminoct02EP.lib</option>
246 <option value="oldff/all_aminont91.lib">oldff/all_aminont91.lib</option>
247 <option value="oldff/all_nucleic02.lib">oldff/all_nucleic02.lib</option>
248 <option value="oldff/protein.amberua.lib">oldff/protein.amberua.lib</option>
249 <option value="oldff/ions91.cmd">oldff/ions91.cmd</option>
250 <option value="oldff/GLYCAM_aminoct_06j_10.lib">oldff/GLYCAM_aminoct_06j_10.lib</option>
251 <option value="oldff/rna.amberua.lib">oldff/rna.amberua.lib</option>
252 <option value="oldff/all_amino02.r1.lib">oldff/all_amino02.r1.lib</option>
253 <option value="oldff/ff02EP.log">oldff/ff02EP.log</option>
254 <option value="oldff/pro-dna91.nmr.off">oldff/pro-dna91.nmr.off</option>
255 <option value="oldff/phosphoaa10.readme">oldff/phosphoaa10.readme</option>
256 <option value="oldff/ff91.log">oldff/ff91.log</option>
257 <option value="oldff/all_aminont2011pol.lib">oldff/all_aminont2011pol.lib</option>
258 <option value="oldff/ff02EP.cmd">oldff/ff02EP.cmd</option>
259 <option value="oldff/all_aminont02.lib">oldff/all_aminont02.lib</option>
260 <option value="oldff/all_amino2011pol.lib">oldff/all_amino2011pol.lib</option>
261 <option value="oldff/ff91.cmd">oldff/ff91.cmd</option>
262 <option value="oldff/all_amino91.lib">oldff/all_amino91.lib</option>
263 <option value="oldff/GLYCAM_aminont_06j_10.lib">oldff/GLYCAM_aminont_06j_10.lib</option>
264 <option value="oldff/lipid11.lib">oldff/lipid11.lib</option>
265 <option value="oldff/all_amino02.lib">oldff/all_amino02.lib</option>
266 <option value="oldff/all_aminoct2011pol.lib">oldff/all_aminoct2011pol.lib</option>
267 <option value="oldff/all_aminont02EP.lib">oldff/all_aminont02EP.lib</option>
268 <option value="oldff/GLYCAM_amino_06j_10.lib">oldff/GLYCAM_amino_06j_10.lib</option>
269 <option value="oldff/all_amino02EP.lib">oldff/all_amino02EP.lib</option>
270 <option value="validate_torsions.py">validate_torsions.py</option>
271 <option value="frcmod.spcfw">frcmod.spcfw</option>
272 <option value="frcmod.ff99SP">frcmod.ff99SP</option>
273 <option value="frcmod.tip4pfb">frcmod.tip4pfb</option>
274 <option value="frcmod.ROC-RNA">frcmod.ROC-RNA</option>
275 <option value="frcmod.constph">frcmod.constph</option>
276 <option value="frcmod.ionsjc_spce">frcmod.ionsjc_spce</option>
277 <option value="frcmod.ions234lm_hfe_tip4pew">frcmod.ions234lm_hfe_tip4pew</option>
278 <option value="frcmod.shaw">frcmod.shaw</option>
279 <option value="frcmod.nma">frcmod.nma</option>
280 <option value="frcmod.ions1lm_iod">frcmod.ions1lm_iod</option>
281 <option value="parm91X.ua.dat">parm91X.ua.dat</option>
282 <option value="frcmod.ionsjc_tip3p">frcmod.ionsjc_tip3p</option>
283 <option value="frcmod.ions234lm_iod_tip3p">frcmod.ions234lm_iod_tip3p</option>
284 <option value="frcmod.ff12SB">frcmod.ff12SB</option>
285 <option value="frcmod.conste">frcmod.conste</option>
286 <option value="lj_1264_pol.dat">lj_1264_pol.dat</option>
287 <option value="frcmod.ions234lm_126_tip4pew">frcmod.ions234lm_126_tip4pew</option>
288 <option value="frcmod.fb15">frcmod.fb15</option>
289 <option value="frcmod.ionslm_126_fb3">frcmod.ionslm_126_fb3</option>
290 <option value="frcmod.phosaa19SB">frcmod.phosaa19SB</option>
291 <option value="frcmod.ff02pol.r1">frcmod.ff02pol.r1</option>
292 <option value="frcmod.ions1lm_1264_tip4pew">frcmod.ions1lm_1264_tip4pew</option>
293 <option value="frcmod.ff99SB">frcmod.ff99SB</option>
294 <option value="frcmod.tip3pfb">frcmod.tip3pfb</option>
295 <option value="frcmod.tip3p">frcmod.tip3p</option>
296 <option value="frcmod.meoh">frcmod.meoh</option>
297 <option value="GLYCAM_06EPb.dat">GLYCAM_06EPb.dat</option>
298 <option value="nucgen.dat">nucgen.dat</option>
299 <option value="frcmod.tip3pf">frcmod.tip3pf</option>
300 <option value="frcmod.opc">frcmod.opc</option>
301 <option value="frcmod.ff19SB_XXX">frcmod.ff19SB_XXX</option>
302 <option value="frcmod.tip4pew">frcmod.tip4pew</option>
303 <option value="frcmod.ff99SB14">frcmod.ff99SB14</option>
304 <option value="frcmod.pol3">frcmod.pol3</option>
305 <option value="frcmod.ff19SB">frcmod.ff19SB</option>
306 <option value="frcmod.ions234lm_hfe_spce">frcmod.ions234lm_hfe_spce</option>
307 <option value="frcmod.ionslm_iod_fb3">frcmod.ionslm_iod_fb3</option>
308 <option value="toyrna.dat">toyrna.dat</option>
309 <option value="frcmod.parmbsc0">frcmod.parmbsc0</option>
310 <option value="frcmod.ff14SB">frcmod.ff14SB</option>
311 <option value="frcmod.tip4pd">frcmod.tip4pd</option>
312 <option value="frcmod.ff03ua">frcmod.ff03ua</option>
313 <option value="frcmod.ionslm_hfe_opc3">frcmod.ionslm_hfe_opc3</option>
314 <option value="opls_parm.dat">opls_parm.dat</option>
315 <option value="frcmod.ionslm_hfe_fb3">frcmod.ionslm_hfe_fb3</option>
316 <option value="frcmod.ff99SBnmr">frcmod.ff99SBnmr</option>
317 <option value="frcmod.ions1lm_1264_tip3p">frcmod.ions1lm_1264_tip3p</option>
318 <option value="frcmod.opc3">frcmod.opc3</option>
319 <option value="frcmod.urea">frcmod.urea</option>
320 <option value="frcmod.phosaa10">frcmod.phosaa10</option>
321 <option value="parmAM1.dat">parmAM1.dat</option>
322 <option value="frcmod.ROC-RNA_const">frcmod.ROC-RNA_const</option>
323 <option value="frcmod.ionslm_hfe_opc">frcmod.ionslm_hfe_opc</option>
324 <option value="frcmod.parmbsc1">frcmod.parmbsc1</option>
325 <option value="parm91.dat">parm91.dat</option>
326 <option value="frcmod.tip5p">frcmod.tip5p</option>
327 <option value="frcmod.ionslm_126_opc">frcmod.ionslm_126_opc</option>
328 <option value="parm10.dat">parm10.dat</option>
329 <option value="parm19ipq.dat">parm19ipq.dat</option>
330 <option value="amberdyes.dat">amberdyes.dat</option>
331 <option value="lipid17.dat">lipid17.dat</option>
332 <option value="frcmod.ionslm_iod_opc3">frcmod.ionslm_iod_opc3</option>
333 <option value="frcmod.ions234lm_1264_tip4pew">frcmod.ions234lm_1264_tip4pew</option>
334 <option value="frcmod.chcl3">frcmod.chcl3</option>
335 <option value="frcmod.parmCHI_YIL">frcmod.parmCHI_YIL</option>
336 <option value="frcmod.ionslm_1264_fb3">frcmod.ionslm_1264_fb3</option>
337 <option value="frcmod.ions1lm_126_spce">frcmod.ions1lm_126_spce</option>
338 <option value="GLYCAM_06j.dat">GLYCAM_06j.dat</option>
339 <option value="frcmod.ff15ipq-m">frcmod.ff15ipq-m</option>
340 <option value="parm99EP.dat">parm99EP.dat</option>
341 <option value="parm94.dat">parm94.dat</option>
342 <option value="parm98.dat">parm98.dat</option>
343 <option value="frcmod.dc4">frcmod.dc4</option>
344 <option value="frcmod.spce">frcmod.spce</option>
345 <option value="frcmod.phosaa14SB">frcmod.phosaa14SB</option>
346 <option value="music.dat">music.dat</option>
347 <option value="parm15ipq_10.3.dat">parm15ipq_10.3.dat</option>
348 <option value="frcmod.ions234lm_126_spce">frcmod.ions234lm_126_spce</option>
349 <option value="frcmod.ions_charmm22">frcmod.ions_charmm22</option>
350 <option value="frcmod.spceb">frcmod.spceb</option>
351 <option value="frcmod.ionslm_iod_fb4">frcmod.ionslm_iod_fb4</option>
352 <option value="frcmod.ionslm_126_fb4">frcmod.ionslm_126_fb4</option>
353 <option value="frcmod.chiOL4">frcmod.chiOL4</option>
354 <option value="gaff.dat">gaff.dat</option>
355 <option value="lipid11.dat">lipid11.dat</option>
356 <option value="all_modrna08.frcmod">all_modrna08.frcmod</option>
357 <option value="frcmod.ions1lm_1264_spce">frcmod.ions1lm_1264_spce</option>
358 <option value="frcmod.ions234lm_1264_tip3p">frcmod.ions234lm_1264_tip3p</option>
359 <option value="frcmod.ff99SBildn">frcmod.ff99SBildn</option>
360 <option value="frcmod.ions1lm_126_tip3p">frcmod.ions1lm_126_tip3p</option>
361 <option value="frcmod.ff14SBmodAA">frcmod.ff14SBmodAA</option>
362 <option value="parm14ipq.dat">parm14ipq.dat</option>
363 <option value="gaff2.dat">gaff2.dat</option>
364 <option value="frcmod.ions234lm_1264_spce">frcmod.ions234lm_1264_spce</option>
365 <option value="frcmod.ionslm_1264_fb4">frcmod.ionslm_1264_fb4</option>
366 <option value="frcmod.ions234lm_iod_tip4pew">frcmod.ions234lm_iod_tip4pew</option>
367 <option value="frcmod.ionsff99_tip3p">frcmod.ionsff99_tip3p</option>
368 <option value="frcmod.vdWall">frcmod.vdWall</option>
369 <option value="frcmod.ions234lm_126_tip3p">frcmod.ions234lm_126_tip3p</option>
370 <option value="frcmod.parmbsc0_ezOL1">frcmod.parmbsc0_ezOL1</option>
371 <option value="frcmod.ionslm_126_opc3">frcmod.ionslm_126_opc3</option>
372 <option value="parm99.dat">parm99.dat</option>
373 <option value="frcmod.ff03">frcmod.ff03</option>
374 <option value="parmPM3.dat">parmPM3.dat</option>
375 <option value="parm96.dat">parm96.dat</option>
376 <option value="lipid14.dat">lipid14.dat</option>
377 <option value="frcmod.ionslm_1264_opc">frcmod.ionslm_1264_opc</option>
378 <option value="parm91X.dat">parm91X.dat</option>
379 <option value="frcmod.DNA.OL15">frcmod.DNA.OL15</option>
380 <option value="frcmod.ions1lm_126_tip4pew">frcmod.ions1lm_126_tip4pew</option>
381 <option value="parm19.dat">parm19.dat</option>
382 <option value="frcmod.ionsjc_tip4pew">frcmod.ionsjc_tip4pew</option>
383 <option value="frcmod.ionslm_hfe_fb4">frcmod.ionslm_hfe_fb4</option>
384 <option value="frcmod.ff99bsc0CG">frcmod.ff99bsc0CG</option>
385 <option value="frcmod.tip4p">frcmod.tip4p</option>
386 <option value="GLYCAM_06h.dat">GLYCAM_06h.dat</option>
387 <option value="frcmod.ions234lm_iod_spce">frcmod.ions234lm_iod_spce</option>
388 <option value="frcmod.ff19SBmodAA">frcmod.ff19SBmodAA</option>
389 <option value="frcmod.protonated_nucleic">frcmod.protonated_nucleic</option>
390 <option value="frcmod.RNA.LJbb">frcmod.RNA.LJbb</option>
391 <option value="opls.info">opls.info</option>
392 <option value="frcmod.phmd">frcmod.phmd</option>
393 <option value="frcmod.ionslm_1264_opc3">frcmod.ionslm_1264_opc3</option>
394 <option value="frcmod.ions234lm_hfe_tip3p">frcmod.ions234lm_hfe_tip3p</option>
395 <option value="frcmod.ionslm_iod_opc">frcmod.ionslm_iod_opc</option>
396 <option value="frcmod.qspcfw">frcmod.qspcfw</option>
397 <option value="frcmod.xFPchromophores">frcmod.xFPchromophores</option>
398 <option value="__pycache__/validate_torsions.cpython-39.pyc">__pycache__/validate_torsions.cpython-39.pyc</option>
399 <option value="leaprc.phosaa10">leaprc.phosaa10</option>
400 <option value="leaprc.protein.ff15ipq">leaprc.protein.ff15ipq</option>
401 <option value="leaprc.phosaa19SB">leaprc.phosaa19SB</option>
402 <option value="leaprc.protein.ff14SB">leaprc.protein.ff14SB</option>
403 <option value="leaprc.water.fb4">leaprc.water.fb4</option>
404 <option value="leaprc.protein.ff19SB_modAA">leaprc.protein.ff19SB_modAA</option>
405 <option value="leaprc.DNA.bsc1">leaprc.DNA.bsc1</option>
406 <option value="leaprc.GLYCAM_06EPb">leaprc.GLYCAM_06EPb</option>
407 <option value="leaprc.amberdyes">leaprc.amberdyes</option>
408 <option value="leaprc.protein.ff15ipq-vac">leaprc.protein.ff15ipq-vac</option>
409 <option value="leaprc.mimetic.ff15ipq">leaprc.mimetic.ff15ipq</option>
410 <option value="leaprc.protein.ff03ua">leaprc.protein.ff03ua</option>
411 <option value="leaprc.gaff2">leaprc.gaff2</option>
412 <option value="leaprc.gaff">leaprc.gaff</option>
413 <option value="leaprc.water.tip3p">leaprc.water.tip3p</option>
414 <option value="leaprc.protein.fb15">leaprc.protein.fb15</option>
415 <option value="leaprc.RNA.YIL">leaprc.RNA.YIL</option>
416 <option value="leaprc.water.tip4pd">leaprc.water.tip4pd</option>
417 <option value="leaprc.lipid17">leaprc.lipid17</option>
418 <option value="leaprc.water.tip4pew">leaprc.water.tip4pew</option>
419 <option value="leaprc.phosaa14SB">leaprc.phosaa14SB</option>
420 <option value="leaprc.lipid14">leaprc.lipid14</option>
421 <option value="leaprc.DNA.OL15">leaprc.DNA.OL15</option>
422 <option value="leaprc.constph">leaprc.constph</option>
423 <option value="leaprc.water.fb3">leaprc.water.fb3</option>
424 <option value="leaprc.water.spce">leaprc.water.spce</option>
425 <option value="leaprc.protein.ff19ipq">leaprc.protein.ff19ipq</option>
426 <option value="leaprc.protein.ff14SB_modAA">leaprc.protein.ff14SB_modAA</option>
427 <option value="leaprc.water.spceb">leaprc.water.spceb</option>
428 <option value="leaprc.ffAM1">leaprc.ffAM1</option>
429 <option value="leaprc.ffPM3">leaprc.ffPM3</option>
430 <option value="leaprc.music">leaprc.music</option>
431 <option value="leaprc.RNA.OL3">leaprc.RNA.OL3</option>
432 <option value="leaprc.conste">leaprc.conste</option>
433 <option value="leaprc.RNA.Shaw">leaprc.RNA.Shaw</option>
434 <option value="leaprc.RNA.LJbb">leaprc.RNA.LJbb</option>
435 <option value="leaprc.modrna08">leaprc.modrna08</option>
436 <option value="leaprc.GLYCAM_06j-1">leaprc.GLYCAM_06j-1</option>
437 <option value="leaprc.protein.ff14SBonlysc">leaprc.protein.ff14SBonlysc</option>
438 <option value="leaprc.water.opc">leaprc.water.opc</option>
439 <option value="leaprc.xFPchromophores">leaprc.xFPchromophores</option>
440 <option value="leaprc.water.opc3">leaprc.water.opc3</option>
441 <option value="leaprc.protein.ff19SB">leaprc.protein.ff19SB</option>
442 <option value="leaprc.protein.ff03.r1">leaprc.protein.ff03.r1</option>
443 <option value="leaprc.RNA.ROC">leaprc.RNA.ROC</option>
444 <option value="oldff/leaprc.ff94.nmr">oldff/leaprc.ff94.nmr</option>
445 <option value="oldff/leaprc.ff84">oldff/leaprc.ff84</option>
446 <option value="oldff/leaprc.ff99SBildn">oldff/leaprc.ff99SBildn</option>
447 <option value="oldff/leaprc.ff99SB">oldff/leaprc.ff99SB</option>
448 <option value="oldff/leaprc.ff98">oldff/leaprc.ff98</option>
449 <option value="oldff/leaprc.ff14SB.redq">oldff/leaprc.ff14SB.redq</option>
450 <option value="oldff/leaprc.rna.ff84">oldff/leaprc.rna.ff84</option>
451 <option value="oldff/leaprc.toyrna">oldff/leaprc.toyrna</option>
452 <option value="oldff/leaprc.rna.ff98">oldff/leaprc.rna.ff98</option>
453 <option value="oldff/leaprc.ff10">oldff/leaprc.ff10</option>
454 <option value="oldff/leaprc.lipid11">oldff/leaprc.lipid11</option>
455 <option value="oldff/leaprc.ff02">oldff/leaprc.ff02</option>
456 <option value="oldff/leaprc.ff02polEP.r0">oldff/leaprc.ff02polEP.r0</option>
457 <option value="oldff/leaprc.ff99">oldff/leaprc.ff99</option>
458 <option value="oldff/leaprc.ff99bsc0">oldff/leaprc.ff99bsc0</option>
459 <option value="oldff/leaprc.GLYCAM_06h-1">oldff/leaprc.GLYCAM_06h-1</option>
460 <option value="oldff/leaprc.rna.ff02EP">oldff/leaprc.rna.ff02EP</option>
461 <option value="oldff/leaprc.rna.ff94">oldff/leaprc.rna.ff94</option>
462 <option value="oldff/leaprc.GLYCAM_06j_10">oldff/leaprc.GLYCAM_06j_10</option>
463 <option value="oldff/leaprc.rna.ff99">oldff/leaprc.rna.ff99</option>
464 <option value="oldff/leaprc.ff86">oldff/leaprc.ff86</option>
465 <option value="oldff/leaprc.ff02polEP.r1">oldff/leaprc.ff02polEP.r1</option>
466 <option value="oldff/leaprc.DNA.bsc0">oldff/leaprc.DNA.bsc0</option>
467 <option value="oldff/leaprc.ff94">oldff/leaprc.ff94</option>
468 <option value="oldff/leaprc.parmbsc0_chiOL4_ezOL1">oldff/leaprc.parmbsc0_chiOL4_ezOL1</option>
469 <option value="oldff/leaprc.ff14SB">oldff/leaprc.ff14SB</option>
470 <option value="oldff/leaprc.GLYCAM_06EP">oldff/leaprc.GLYCAM_06EP</option>
471 <option value="oldff/leaprc.GLYCAM_04">oldff/leaprc.GLYCAM_04</option>
472 <option value="oldff/leaprc.ff02pol.r0">oldff/leaprc.ff02pol.r0</option>
473 <option value="oldff/leaprc.GLYCAM_06h-12SB">oldff/leaprc.GLYCAM_06h-12SB</option>
474 <option value="oldff/leaprc.rna.ff02">oldff/leaprc.rna.ff02</option>
475 <option value="oldff/leaprc.ff14ipq">oldff/leaprc.ff14ipq</option>
476 <option value="oldff/leaprc.GLYCAM_06h">oldff/leaprc.GLYCAM_06h</option>
477 <option value="oldff/leaprc.ff96">oldff/leaprc.ff96</option>
478 <option value="oldff/leaprc.GLYCAM_06">oldff/leaprc.GLYCAM_06</option>
479 <option value="oldff/leaprc.ff99SBnmr">oldff/leaprc.ff99SBnmr</option>
480 <option value="oldff/leaprc.ff02pol.r1">oldff/leaprc.ff02pol.r1</option>
481 <option value="oldff/leaprc.ff03">oldff/leaprc.ff03</option>
482 </param>
483 </xml>
484 <xml name="addingions">
485 <param name="arg_variable" label="Variable name of UNIT:" type="text" value="" help="The variable name that your system's components are assigned to."/>
486 <param name="arg_ion1" label="ion1 type" type="text" value="" help="Atom type for ion, as written in your chosen forcefield file. For example, choose Cl- for chloride."/>
487 <param name="arg__ion1" label="# of ion1 atoms to add" type="text" value="" help="Type 0 if you want to add enough ions to neutralize (if using the conventional 'addIons' command)."/>
488 <param name="arg_ion2" label="ion2 type" type="text" value="" help="Atom type for ion, as written in your chosen forcefield file. For example, choose Na+ for sodium."/>
489 <param name="arg__ion2" label="# of ion1 atoms to add" type="text" value="" help="Type 0 if you want to add enough ions to neutralize (if using the conventional 'addIons' command)."/>
490 </xml>
491 <xml name="unitvariable">
492 <param name="arg_unit" label="Variable name of UNIT:" type="text" value="" help="This is the variable name for the target UNIT, which can be a protein, ligand, or any other unique molecular component of the system, that is loaded into LEaP. "/>
493 </xml>
494 <xml name="container">
495 <param name="arg_container" label="container value" type="text" value="" help="UNIT/RESIDUE/ATOM to apply this to"/>
496 </xml>
497 <xml name="create">
498 <param name="createVar_assign" label="Assign to variable named" type="text" value=""/>
499 <param name="arg_name" label="name" type="text" value="" help="STRING"/>
500 </xml>
501 <xml name="object">
502 <param name="arg_obj" label="obj value" type="text" value="" help="The object can be an entire UNIT, or use periods to choose specific RESIDUES (UNIT.RESIDUE#) and/or ATOMS (UNIT.RESIDUE#.ATOMname) within it." />
503 </xml>
504 <xml name="newfile">
505 <param name="newfile" label="new file to save data into" type="text" />
506 </xml>
507 <xml name="loadfile" token_data_format="txt">
508 <param name="arg_filename" label="File" type="data" format="@DATA_FORMAT@" />
509 </xml>
510 <xml name="defaultsettings">
511 <param name="settingsvariable" label="Parameter to adjust" type="select" value="" help="">
512 <option value="PdbWriteCharges">PdbWriteCharges</option>
513 <option value="OldPrmtopFormat">OldPrmtopFormat</option>
514 <option value="Gibbs">Gibbs</option>
515 <option value="UseResIds">UseResIds</option>
516 <option value="Charmm">Charmm</option>
517 <option value="DeleteExtraPointAngles">DeleteExtraPointAngles</option>
518 <option value="FlexibleWater">FlexibleWater</option>
519 <option value="PBRadii">PBRadii</option>
520 <option value="Dielectric">Dielectric</option>
521 <option value="dipole_damp_factor">dipole_damp_factor</option>
522 <option value="sceescalefactor">sceescalefactor</option>
523 <option value="scnbscalefactor">scnbscalefactor</option>
524 <option value="CMAP">CMAP</option>
525 <option value="PHIPSIMAP">PHIPSIMAP</option>
526 <option value="ipol">ipol</option>
527 <option value="nocenter">nocenter</option>
528 <option value="reorder_residues">reorder_residues</option>
529 </param>
530 </xml>
531 <xml name="settingoptions">
532 <param name="usersetting" label="setting" type="select" help="If unsure of what to choose, please refer to the 'help' message for this command by scrolling down this page, to see which settings apply to each command.">
533 <option value="on">ON</option>
534 <option value="off">OFF</option>
535 <option value="bondi">bondi</option>
536 <option value="mbondi">mbondi</option>
537 <option value="mbondi2">mbondi2</option>
538 <option value="mbondi3">mbondi3</option>
539 <option value="parse">parse</option>
540 <option value="pbamber">pbamber</option>
541 <option value="amber6">amber6</option>
542 <option value="distance">distance</option>
543 <option value="constant">constant</option>
544 <option value="real">real</option>
545 <option value="integer">integer</option>
546 </param>
547 </xml>
548 <xml name="solvateparams">
549 <param name="arg_solute" label="solute UNIT" type="text" value="" help="This is the variable name for the target UNIT, which can be a protein, ligand, or any other unique molecular component of the system that is loaded into LEaP and you are now trying to solvate. "/>
550 <param name="arg_solvent" label="solvent UNIT" type="text" value="" help="The UNIT name for the water model you would like to use. Options include TIP3PBOX, TIP4PBOX, TIP4PEWBOX, and TIP5PBOX. "/>
551 <param name="arg_buffer" label="buffer value" type="text" value="" help="object"/>
552 <param name="arg_closeness" label="closeness value" type="text" value="" help="This is used to control the extent to which solvent atoms overlap solute atoms. The default value is 1.0, which allows no overlap. "/>
553 </xml>
554 <xml name="amberfiles_conditional">
555 <conditional name="file_source">
556 <param name="file_source_selector" type="select" label="Select file source">
557 <option value="history">From history</option>
558 <option value="builtin">From Built-in AmberTools data</option>
559 </param>
560 <when value="history">
561 <expand macro="loadfile" />
562 </when>
563 <when value="builtin">
564 <expand macro="builtin_amberfiles" />
565 </when>
566 </conditional>
567 </xml>
568 <xml name="citations">
569 <citations>
570 <citation type="doi">10.1002/jcc.20290</citation>
571 <citation type="bibtex">
13 @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. 572 @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A.
14 Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, 573 Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo,
15 J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url = 574 J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url =
16 {http://ambermd.org/CiteAmber.php}, }</citation> 575 {http://ambermd.org/CiteAmber.php}, }</citation>
17 <yield/> 576 <yield/>
18 </citations> 577 </citations>
19 </xml> 578 </xml>
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21 <citation type="doi">10.1021/ct300418h</citation> 580 <citation type="doi">10.1021/ct300418h</citation>
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