[gmx-users] phosphated residue

[David van der Spoel]

tonglei wrote:
> 
> Dear all
>      There is a phosphate tyr in my protein, so when pdb2gmx, the fatal 
> error is "atom p is not found"
>   
>        How to deal  with this problem? how to add the topology file of 
> phosphate ion to residue database?

chapter 5 of the manual.

you will have to find parameters somewhere in the literature, or develop 
your own.
>   
>      Thank you very much
> 
> -- 
> Na Zhang
> Chemistry Department
> Zhejiang University PRC
> xbcdnana at gmail.com <mailto:xbcdnana at gmail.com>
> 
> 
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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://folding.bmc.uu.se
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