[gmx-users] Missing Residues are list ind pdb file

[Tsjerk Wassenaar]

Hi Jack,

On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
> I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the
> non-standard residues. Re-named n-terminal and c-terminal residues. Took out
> connects because that worked last time though I'm uncertain if connect
> really maters.

Thank god you didn't went up a hill to dance under the full moon. You
might have thought that that was also part of solving your error and
would only be preparing structures once a month then!

> Another issue with preping a protein. Its says I a missing H and HA for this
> residue, but have those atoms listed there. Why does it say CYSH instead of
> CYS2 on residue 15 ???

Well, the closest other CYS-SG is 0.287 nm:

 CYS2414 SG18376   0.287   1.574   2.660   2.205   1.101   2.402   1.361

That is well beyond the cut-off used for assigning SS bonds, so it
must be a stand-alone, protonated cysteine (CYSH).

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist