[gmx-users] Problem about *pdbgmx

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 13 12:12:17 CET 2008

sudheer babu wrote:
> Hi gmx-users,
> I want to protonate only HIS residues in  my protein , so  I gave 
> command like this *pdb2gmx  -f protein.pdb -HIS then it asked which 
> number of HIS to protonate, I gave numbers of HIS residues which I want 
> protonate , it ran fine without error, but when I open conf.gro file, 
> along with HISH, LYS also protonating and form LYSH. In input file LYS 
> present like this. Why it happening like this?

that's default. use -lys flag and -arg and -glu and -asp

>  Pls help me.
> Thanks in advance.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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