[gmx-users] amino acids in unusual protonation states

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 19 22:28:58 CET 2001

On Wed, 19 Dec 2001, Markus Metz wrote:

>Hi all,
>I was wondering how I could deprotonate for example the sulphur in a
>Cystein. I was checking the pdb2gmx man page and the amino acids Lys, Asp,
>Glu, His are changeable. 
>Sorry if this is a FAQ.
Hm, there is no database entry in ff*.rtp for it. Maybe you can add one
e.g. CYS- (have to make an entry in ff*rtp and ff*hdb)
with a charge of -1 on the sidechain. If you rename the residue to CYS- 
in the pdb file pdb2gmx will automatically find it.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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