[gmx-users] position restrain energy

[Nikhil Maroli]

Hi thanks for your suggestion,

When i give both same name in mdp and top it gives an error

Atom index (123) in position_restraints out of bounds (1-122).
This probably means that you have inserted topology section "position_restraints


this is my topology file structure
; Include forcefield parameters
#include "toppar/charmm36.itp"

#include "toppar/PROA.itp"
#include "toppar/PROB.itp"
#include "toppar/PROC.itp"
#include "toppar/PROD.itp"
#include "toppar/PROE.itp"
#include "toppar/PROF.itp"
#include "toppar/PROG.itp"
#include "toppar/PROH.itp"
; Ligand position restraints
#ifdef POSRES_PROT
#include "posre_cpn.itp"
#endif

#include "toppar/POPE.itp"
#include "toppar/TIP3.itp"
#include "toppar/SOD.itp"
#include "toppar/CLA.itp"



PROA....PROH  are identical cyclic peptide rings ,posre_cpn is restrain file
for c-alpha atoms in all the rings .

in mpd file
define      = -DPOSRES_PROT

when i give only
define      = -DPOSRES

in mdp grompp running successfully but in gmx energy no restrain energy --