[gmx-users] selecting res CYS from G53a5 using pdb2gmx
ppirzade at ucalgary.ca
Wed Jan 9 00:09:42 CET 2013
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:
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?
Sorry for inconveniences.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 3:55 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 1:37 AM, Payman Pirzadeh wrote:
> Dear Justin,
> Thanks for your suggestions. It all made sense.
> But I ran into a strange problem. I checked the mail list, and all I
> found was about misspelling the force field name. I copied the whole
> gromos53a5.ff directory into my working folder, copied the modified
> .rtp, .dat and .hdb files into the gromos53a5.ff folder, and issued:
> pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro
> -inter -ff gromos53a5.ff but what I got was:
> Program pdb2gmx_d_mpi, VERSION 4.5.4
> Source code file: pdb2top.c, line: 239
> Fatal error:
> Could not find force field 'gromos53a5.ff' in current directory,
> install tree or GMXDATA path.
> For more information and tips for troubleshooting, please check the
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> If I do not add the -ff option, the default pdb2gmx command works, by
> opening the force field from the default path. I tried 'source GMXRC'
> from my working folder, but same error pops up. I am not sure what I
> am missing here?!
You're using the wrong syntax. The option -ff should take just the prefix
of the force field directory, i.e. "-ff gromos53a5" which causes pdb2gmx to
search for a gromos53a5.ff directory.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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