Mercurial > repos > chemteam > gmx_setup

changeset 4:b43abebffad6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:50:01 -0400
parents 4c48f2526697
children 35b314fe6c90
files macros.xml setup.xml
diffstat 2 files changed, 56 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Aug 30 15:06:44 2019 -0400
+++ b/macros.xml	Mon Oct 07 12:50:01 2019 -0400
@@ -1,8 +1,8 @@
 <macros>
-    <token name="@VERSION@">2019.1</token>
+    <token name="@VERSION@">2019.1.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">gromacs</requirement>
+            <requirement type="package" version="2019.1">gromacs</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -11,32 +11,46 @@
         </citations>
     </xml>
     <xml name="md_inputs">
+        <param argument="traj" type="select" label="Trajectory output">
+            <option value='none'>Return no trajectory output</option>
+            <option value='xtc'>Return .xtc file (reduced precision)</option>
+            <option value='trr'>Return .trr file (full precision)</option>
+            <option value='both'>Return both .xtc and .trr files</option>
+        </param>
+
+        <param argument="str" type="select" label="Structure output">
+            <option value='none'>Return no structure output</option>
+            <option value='gro'>Return .gro file</option>
+            <option value='pdb'>Return .pdb file</option>
+            <option value='both'>Return both .gro and .pdb files</option>
+        </param>
+
         <conditional name="mdp">
             <param name="mdpfile" type="select" label="Parameter input">
                 <option value="custom">Upload own MDP file</option>
                 <option value="default">Use default (partially customisable) setting</option>
             </param>
             <when value="custom">
-                <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/>
+                <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
             </when>
             <when value="default">
-                <param argument="integrator" type="select" label="Choice of integrator.">
+                <param argument="integrator" type="select" label="Choice of integrator">
                     <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
                     <option value="sd">Stochastic dynamics integrator</option>
                     <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
                 </param>
-                <param argument="constraints" type="select" label="Bond constraints (constraints).">
+                <param argument="constraints" type="select" label="Bond constraints (constraints)">
                     <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
                     <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
                     <option value="all-bonds">All bonds (all-bonds).</option>
                     <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
                     <option value="all-angles">All bonds and angles (all-angles).</option>
                 </param>
-                <param argument="cutoffscheme" type="select" label="Neighbor searching.">
+                <param argument="cutoffscheme" type="select" label="Neighbor searching">
                     <option value="Verlet">Generate a pair list with buffering.</option>
                     <option value="group">Generate a pair list for groups of atoms.</option>
                 </param>
-                <param argument="coulombtype" type="select" label="Electrostatics.">
+                <param argument="coulombtype" type="select" label="Electrostatics">
                     <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
                     <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
                     <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
@@ -48,27 +62,13 @@
                 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
                 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
                 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
-                <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" />
+                <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
                 
             </when>
 
         </conditional>
-        
-        <param argument="traj" type="select" label="Trajectory output.">
-            <option value='none'>Return no trajectory output</option>
-            <option value='xtc'>Return .xtc file (reduced precision)</option>
-            <option value='trr'>Return .trr file (full precision)</option>
-            <option value='both'>Return both .xtc and .trr files</option>
-        </param>
 
-        <param argument="str" type="select" label="Structure output.">
-            <option value='none'>Return no trajectory output</option>
-            <option value='gro'>Return .gro file</option>
-            <option value='pdb'>Return .pdb file</option>
-            <option value='both'>Return both .gro and .pdb files</option>
-        </param>
-
-        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
+        <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
 
 
     </xml>
--- a/setup.xml	Fri Aug 30 15:06:44 2019 -0400
+++ b/setup.xml	Mon Oct 07 12:50:01 2019 -0400
@@ -16,8 +16,8 @@
 
     <inputs>
         <!-- PDB2GMX VARS -->
-        <param argument="pdb_input" type="data" format='pdb' label="PDB input file."/>
-        <param argument="water" type="select" label="Water model" help="">
+        <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/>
+        <param argument="water" type="select" label="Water model" help="Model for simulating water molecules in the solvent">
             <option value="tip3p" selected="true">TIP3P</option>
             <option value="tip4p">TIP4P</option>
             <option value="tips3p">TIPS3P</option>
@@ -27,7 +27,7 @@
             <option value="none">None</option>
         </param>
 
-        <param argument="ff" type="select" label="Force field">
+        <param argument="ff" type="select" label="Force field" help="Specify a molecular force field">
             <option value="oplsaa" selected="true">OPLS/AA</option>
             <option value="gromos43a1">GROMOS43A1</option>
             <option value="amber96">AMBER96</option>
@@ -48,7 +48,7 @@
         <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." />
         
         <!-- EDITCONF VARS -->
-        <param argument="box_d" type="float" label="Box dimensions in nanometers." value="0.0" min="0.0" max="10.0" help="Box dimensions" />
+        <param argument="box_d" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="10.0" help="Dimensions of the box in which simulation will take place" />
         <param argument="box_type" type="select" label="Box type"
             help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times.">
             <option value="cubic">Rectangular box with all sides equal</option>
@@ -57,7 +57,7 @@
             <option value="octahedron">truncated octahedron</option>
         </param>
 
-        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
+        <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
 
     </inputs>
     <outputs>
@@ -83,7 +83,34 @@
     </tests>
     <help><![CDATA[
 
-Initial GROMACS setup. Upload a structure in PDB format and produce a topology and a structure in GRO format contained in a box of defined shape and dimensions.
+.. class:: infomark
+
+**What it does**
+
+This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command and also defining a simulation box with editconf.
+
+Please note that the tool will only successfully generate a topology for residues it recognizes (i.e. standard amino acids). If the structure contains other components such as ligands, these should be separately parameterized with the AmberTools or ACPYPE tools. In this case, make sure to also use an AMBER forcefield for this tool to ensure compatability with the ligand topology. 
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - PDB file.
+       - Water model and forcefield must be specified.
+       - Parameters for the simulation box (dimensions and shape).
+     
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - GROMACS topology (TOP) file.
+       - Position restraint (itp) file, which may be useful for system equilibration.
+       - GRO structure file.
 
     ]]></help>