[gmx-users] amino acids in unusual protonation states

[K.A.Feenstra]

David van der Spoel wrote:
> 
> 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.


However, that will just be a rough guess to the 'proper' forcefield
parameters for this group. Optimizing them is important, but not at
all trivial...


-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
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