[gmx-users] big protein dynamics with gromacs 3.2.1

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 29 22:24:48 CET 2005

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
>>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.
> 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 
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 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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