[gmx-users] big protein dynamics with gromacs 3.2.1

[Tsjerk Wassenaar]

Hi Adriana,

If you have the file in the working directory, that instance of the file
will take precedence.
As for the SOL SOL SOL.., I'm not sure where it comes from. Did you add
solvent to an already solvated system? The important thing is that the total
number of solvent molecules and the order of molecules in the .top file and
the structure file match.

Cheers,

Tsjerk

On 11/29/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Adriana Pietropaolo wrote:
> > On Tue, 29 Nov 2005, Tsjerk Wassenaar wrote:
> >
> >
> >>Hi Adriana,
> >>
> >>pdb2gmx should be able to detect SS bonds automatically, though in some
> >>cases fails to do so (if the distance is too large). If you know that
> you're
> >>missing a SS bond you can add an entry to the file specbond.dat in the
> >>directory $GMXDIR/share/top (maybe first copy the file to your
> directory).
> >>Copy the line referring to the cys-bridge and change the distance to the
> >>distance in your structure. Running through pdb2gmx should then fix your
> >>problem.
> >>
> >>With regards to the other issue, neither editconf nor genbox changes
> your
> >>structure (there's no cutting). There may be shifts over the periodic
> >>boundaries, but these don't affect the resulting simulation system.
> >>
> >>Cheers,
> >>
> >>Tsjerk
> >>
> >
> > Thanks a lot,
> > I would like to ask you if there is a flag (like pdb2gmx
> > -...) so that pdb2gmx can read in local specbond.dat,
> > because I can't modify this file in the  root directory,
> > so I copied this file in my home directory.
> You can put the modified files in a specific dir, and set an environment
> variable:
> setenv GMXLIB /home/adriana/top
> or something like that.
> > As regarding with the other question for a sample already with water
> > molecules, why pdb2gmx generates a topology with 3 solvent group like
> SOL
> > SOL SOL? the water molecules are 29915 and the pdb generated from MD
> > simulation is divided in layers and not uniformly solvated...
> >  Thanks in advance,
> > Adriana
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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