Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz <j...@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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
