[gmx-users] selecting res CYS from G53a5 using pdb2gmx

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jan 9 00:22:52 CET 2013

These are the lines in my residuetype.dat:
CYS     Protein
CYS1    Protein
CYS2    Protein
CYSH    Protein
CYA     Protein
DALA    Protein

Have I missed anything? How can I couple CYA with protein under this


-----Original Message-----
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
strange behavior?

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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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