[gmx-users] Position restraints

Tom Dupree t.dupree at unsw.edu.au
Thu Jun 16 03:54:50 CEST 2011


Greetings all,

I have run into a little bit of a problem.

I am trying to simulate a hetro-dimer. Through previous work we have identified 302  C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr.
However when I get to the simulation step I can't get grompp to work.

I ran

genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr

As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range. 

Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files?  Furthermore can I actually do a constraint matrix over multiple molecules?

Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) 


All the best,

Tom


Fatal error:
[ file subset.itp, line 145 ]:
Atom index (5222) in constraints out of bounds (1-5149).
This probably means that you have inserted topology section "constraints"
in a part belonging to a different molecule than you intended to.
In that case move the "constraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

My topology file
;
;	File 'topol.top' was generated
;	By user: onbekend (0)
;	On host: onbekend
;	At date: Tue May 31 11:44:23 2011
;
;	This is a standalone topology file
;
;	It was generated using program:
;	pdb2gmx - VERSION 4.5.3
;
;	Command line was:
;	pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v 
;
;	Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "topol_Protein_chain_A2.itp"
#ifdef POSRES
#include "posre_Protein_chain_A2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B2.itp"
#ifdef POSRES
#include "posre_Protein_chain_B2.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B3.itp"
#ifdef POSRES
#include "posre_Protein_chain_B3.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
#include "topol_Protein_chain_B4.itp"
#ifdef POSRES
#include "posre_Protein_chain_B4.itp"
#endif
#ifdef REST
#include "subset.itp"
#endif
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