[gmx-users] position restrain energy

[Justin Lemkul]

On 4/18/16 9:05 AM, Nikhil Maroli wrote:
> 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
>

You can't do this.  Restraints are applied on a per-moleculetype basis.

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

> #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 --
>

Because it's doing precisely nothing, so no error can be raised and no 
restraints are applied because of the mismatch between define and #ifdef.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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