[gmx-users] selecting res CYS from G53a5 using pdb2gmx
ppirzade at ucalgary.ca
Wed Jan 9 00:58:54 CET 2013
Found my solution; made an index file which had the protein and CYA in the
Thanks for all your helps Justin.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 4:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 6:09 PM, Payman Pirzadeh wrote:
> Dear Justin,
> Thanks for the tips. Things worked smoothly up to the point when I
> wanted to run an actual simulation. When I wanted to run grompp for a
> NVT simulation, I got this error message:
> Fatal error:
> 7 atoms are not part of any of the T-Coupling groups
> I realized that that in my mdp file, I had:
> Tcoupl = Nose-Hoover
> tau_t = 0.2 0.2 0.2
> tc-grps = Protein SOL CL-
> ref_t = 310 310 310
> I noticed that this warning is related to the CYA residue. So I added
> CYA as a new group to the above list and problem was solved. But what
> remains strange/scary to me is that I defined CYA in residuetypes.dat!
> Shouldn't grompp consider the new residue as part of the protein?
> Won't this separate temperature coupling of a residue and protein cause
Yes, as does the fact that you're coupling ions separately from the solvent.
If you correctly added CYA to residuetypes.dat, this shouldn't happen. Do
not couple it separately from the protein; that makes no sense.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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