[gmx-users] atoms are not part of any of the T-Coupling groups

[Justin Lemkul]

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"
> #endif
>
> 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
> #endif
>
> 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:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
>
> 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 
to suggest.

-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

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