[gmx-users] atoms are not part of any of the T-Coupling groups
jalemkul at vt.edu
Wed Aug 6 16:37:07 CEST 2014
On 8/6/14, 3:46 AM, Nidhi Katyal wrote:
> Hello all,
> I am working on protein with two chains. I would like to restrain one atom
> of one chain while doing steered MD. For the same reason, I have created an
> index file that includes that atom, then created its posre.itp file and
> finally included following lines at the end of topol_Protein_chainA.itp:
> ; Include Position restraint file
> #ifdef POSRES_CA_chA_r131
> #include "posre.itp"
> I am also pasting a small section of my topol.top file:
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Ion_chain_A2.itp"
> #include "topol_Ion_chain_B2.itp"
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> After carrying out NPT equilibration, when I run following command:
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
> -o pull.tpr
> as given in tutorial:
> I am getting following error:
> 215400 atoms are not part of any of the T-Coupling groups
> Since my pull.mdp file as the same as given in tutorial, my coupling
> groups are Protein and Non-Protein.
> I suspect there is something wrong while adding restraints using
> include file mechanism. Please help me resolve the problem.
The error is not a result of the #include mechanism; it's a problem in the group
definitions, either in the .mdp file or in the index file. Without the full
text of the .mdp and the gmxcheck output of the index.ndx file, there's little
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
More information about the gromacs.org_gmx-users