[gmx-users] The file

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 14 21:39:08 CEST 2006

Elias santos wrote:
> HI! I have a problem.
>  I am working with a molecule that will count two clusters, co-ordinated 
> for cysteins.
> But in the pdb file does not exist linkings between iron atoms and of 
> the cystens, even so literature affirms that it exists.
> How I can edit this file?
>  Therefore when I edited it even so it has if visualized the linkings in 
> this format (pdb), when processing it with pdb2gmx the linkings 
> between irons and atoms SG of the cisteínas these linkings do not appear 
> in the topology archive. What it can be?

such clusters are not supported out of the box. you will have to make 
your own. chapter 5 in the manual.
> E, Silva
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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://folding.bmc.uu.se

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