[gmx-users] Missing Residues are list ind pdb file
tsjerkw at gmail.com
Sun Jan 17 10:18:10 CET 2010
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).
Tsjerk A. Wassenaar, Ph.D.
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