Dear gmx-users,<br><div class="gmail_quote"><br>I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message:<br>
<br>Program grompp, VERSION 3.3<br>Source code file: toppush.c, line: 1108<br><br>Fatal error:<br>[ file "posre_entirelipid1.itp", line 56 ]:<br> Atom index (53) in position_restraints out of bounds (1-52)<br>
<br>I sent an email about this yesterday, but the advice was not applicable because of the set-up of my topology file.<br><br><font size="1">previous advice: **********************<br>Position restraints sections must be placed within the same [ moleculetype ] definition. So, you can't include all of the position restraint information in one file, since that file is part of the Protein [ moleculetype ] definition. The ligand should be placed in its own posre.itp file and included in the topology.<br>
<br>These lines must be placed *outside* of the [ moleculetype ] directive of any other molecule(s) in the system. For consistency, whenever I have ligands, I place them immediately after the protein [ moleculetype ] and water topology, i.e.:<br>
<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>#include "ligand.itp"<br><br>#ifdef POSRES_LIGAND<br>#include "ligand_posre.itp"<br>#endif<br><br>#include "spc.itp"<br><br>
(etc).<br><br>That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand section begins with #include "ligand.itp", ends with the POSRES_LIGAND section, and then the topology reads the water topology, etc.<br>
*********************************************************************<br><br></font>This is the structure of my main topology file:<br><br>
<pre>; Include forcefield parameters
#include "ffoplsaa.itp"
; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"
#include "topol_D.itp"
; Include lipid topology
#include "popc_Stockner.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
POPC 288
SOL 33722
NA+ 28</pre>***************<br><br>At the end of the lipid topology file popc_Stockner.itp, I have placed the #include for the lipid position restraint file posre_lipid.itp. I tried moving the #include for the lipid position restraint into the main topology file, directly after the include lipid topology line, but this gives me the same error.<br>
<br>Do you have any suggestions of where exactly to put the #include for the lipid position restraint?<br><br>Thank you very much<br>
<br></div><br>