[gmx-users] Error in Ligand position restraints

[Justin Lemkul]

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 ]
> ; Name            nrexcl
> 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       fcx        fcy        fcz
>     1    1       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
> POPC    128
>
>
> 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================