[gmx-users] the different protonation state of HIS

[Peter C. Lai]

On 2012-04-05 08:55:24PM +0800, lina wrote:
> On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett <acootbrett at yahoo.com> wrote:
> > Dear All,
> >
> > For the different protonation state of HIS, what are there 3-letter code for

This is also somewhat forcefield dependent (and how you name the histidines
in the PDB as well).

> > GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me
> > to read? Do we still have any other confusing amino acids?

-SH will show up as part of a -SH containing residue (cysteine).
pdb2gmx will attempt to ask you about -S-S- bridges correctly if two 
cysteines are close to each other, use the -ss parameter to pdb2gmx. The 
manual has a description of how to force a disulfide bridge using 
specbond.dat if the starting structure is suboptimal...