Ok. My topology:<br><br>; Include forcefield parameters<br>#include "./charmm27.ff/forcefield.itp"<br><br>; Include ligand topology<br>#include "ligand1.itp"<br><br>; Include Position restraint file<br>
#ifdef POSRES_1<br>#include "posre_ligand1.itp"<br>#endif<br><br>; Include ligand topology<br>#include "ligand2.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES_2<br>#include "posre_ligand2.itp"<br>
#endif<br><br>; Include ligand topology<br>#include "ligand3.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES_3<br>#include "posre_ligand3.itp"<br>#endif<br><br>; Include ligand topology<br>
#include "ligand4.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES_4<br>#include "posre_ligand4.itp"<br>#endif<br><br><br>; Include ligand topology<br>#include "ligand5.itp"<br>
<br>; Include Position restraint file<br>#ifdef POSRES_5<br>#include "posre_ligand5.itp"<br>#endif<br><br>; Include ligand topology<br>#include "ligand6.itp"<br><br>; Include Position restraint file<br>
#ifdef POSRES_6<br>#include "posre_ligand6.itp"<br>#endif<br><br>; Include water topology<br>#include "./charmm27mod.ff/tip3p.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>
[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include topology for ions<br>#include "./charmm27.ff/ions.itp"<br><br>[ system ]<br>
; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound #mols<br>ligand1 1<br>ligand2 1<br>ligand3 1<br>ligand4 1<br>ligand5 1<br>ligand6 1<br>
SOL 4617<br><br><br>Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information is the same<br><br>posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.<br><br>Then when I grompp: <br>
<br>Syntax error - File ligand2.itp, line 7<br>Last line read:<br>'[ atomtypes ] '<br>Invalid order for directive atomtypes<br><br>Any suggestions appreciated,<br><br>Steven<br><br><br><br><br><div class="gmail_quote">
On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 5/28/12 10:48 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
I am fighting with the position restraints. My system cosnsists of 6 ligands -<br>
all of them have the same topology - ligand.itp. I want to:<br>
<br>
1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre<br>
ligand1.itp<br>
2. Restrain 5 of them and pull one of them away.<br>
<br>
Here I came across some difficulties.<br>
<br>
I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp<br>
<br>
and by index files I create an index of the ligands I wan to restrain. Each my<br>
ligands has 46 atoms. When I process to grompp:<br>
<br>
Atom index (256) in position_restraints out of bounds (1-46).<br>
This probably means that you have inserted topology section "position_restraints<br>
<br>
Shall I rename Ligands as different residue names? If my posre includes 1-46<br>
atom all ligands are restraints? How to restrain just 5 out of 6 of them?<br>
<br>
</blockquote>
<br></div></div>
Position restraints are applied on a per-moleculetype basis. If you have six copies of a ligand, the only way to do this is to define the sixth as a special [moleculetype] (even if it contains identical information) with a different name, such that it can be restrained in the absence of restraints on the others. See the logic here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#Atom_<u></u>index_n_in_position_<u></u>restraints_out_of_bounds</a><br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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</font></span></blockquote></div><br>