[gmx-users] atoms not part of any of the T-coupling groups
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 24 21:42:46 CEST 2008
Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group
Protein_Zn2+)? Coupling ions separately often leads to weird
behavior/explosions when they're free in the solvent. I've never dealt with
proteins that have ions bound, so I'm curious to see what everyone else thinks
about this, just as a point of curiosity.
-Justin
Andy Shelley wrote:
> Garry,
>
> I believe you are trying to not temperature couple the 4 zincs. To do
> this put the 4 zincs in one group and include that group in the listing
> of tc_grps and then correspondingly assign tau_t. tau_t=0 means no
> temperature coupling, but I think you will also need to give a
> temperature for the tau_t=0 even though that group does not have
> temperature coupling. See section 7.3.13 in the gromacs user manual.
>
> Andy
>
> garry wrote:
> >
> > I am a novice at Gromacs (although I used Gromos 20+ years ago!)....I
> > have a dimer with two zincs per monomer, and I get the following
> > complaint when running the grompp with pr.dmp, which I assume is
> > referring to the 4 zincs.
> >
> >
> > There are: 6789 OTHER residues
> > There are: 262 PROTEIN residues
> > There are: 0 DNA residues
> > Analysing Protein...
> > Analysing Other...
> >
> > ------------------------------
> -------------------------
> > Program grompp, VERSION 3.3.2
> > Source code file: readir.c, line: 865
> >
> > Fatal error:
> > 4 atoms are not part of any of the T-Coupling groups
> > -------------------------------------------------------
> >
> > the zincs are in the pdb file as (properly formatted in the pdb file!):
> >
> > ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00
> > 51.42 S
> > ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00
> > 50.50 C
> > ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00
> > 50.69 O
> > HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00
> > 43.80 ZN
> > HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00
> > 38.99 ZN
> > HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00
> > 28.52 ZN
> > HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00
> > 32.42 ZN
> >
> > What am I doing wrong ?
> >
>
> What does your .mdp file look like? Have you included the Zn2+ within
> one of
> your tc-grps?
>
> -Justin
>
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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