On 8/6/14, 3:03 AM, neha bharti wrote:
Hello All
I am trying to perform MD for protein ligand protein complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I successfully performed till
perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
After this when I started performing energy minimization part it gives
error :
Fatal error:
[ file strong_posre.itp, line 6979 ]:
Atom index (6975) in position_restraints out of bounds (1-6974).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
I think the problem is that I have included position restraints for protein
in topology file but not includes position restraints for ligand in that
file.
when I added
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
to my topology file it consider both protein and ligand so the number of
residue present in my position restraint file and Strong position restraint
is different.
I also check it by adding position restraint for ligand in my topology
file. but it still giving the same error.
I also check by merging position restraint file for ligand and protein but
the same error is present.
This is my topology file:
; Include forcefield parameters
#include "charmm36_lipid.ff/forcefield.itp"
; Include ligand topology
#include "lig.itp"
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
...
...
...
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Ligand position restraints
#ifdef POSRES
#include "posre_lig.itp"
#endif
The topology is organized incorrectly. A [position_restraints] directive must
be declared immediately after the [moleculetype] to which it belongs, using the
atom numbering of the [moleculetype], NOT the global numbering.
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
; Include POPC chain topology
#include "popc.itp"
; Include water topology
#include "charmm36_lipid.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcxfcyfcz
11 1000 1000 1000
#endif
; Include topology for ions
#include "charmm36_lipid.ff/ions.itp"
[ system ]
; Name
Gyas ROwers Mature At Cryogenic Speed
[ molecules ]
; Compound#mols
Protein 1
lig 1
POPC128
I have also check by changing the position of lig.itp file and posre_lig
file by keeping them together like
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "lig.itp"
; Ligand position restraints
#ifdef POSRES
#include "posre_lig.itp"
#endif
then it gives another error because of the change in position of ligand
topology file.
Fatal error:
Syntax error - File cyc.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
The ligand topology must be declared immediately after the #include statement
for the force field if it introduces new atom types. Thus, the position
restraint file must be moved up accordingly.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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