[gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 17 19:42:38 CEST 2009
chris.neale at utoronto.ca wrote:
> The inability to search the archives is certainly leading to some
> redundancy. I use google now, it does a decent job of digging up stuff
> from the gmx mailing list archives -- Even the oldwww search link takes
> me to the new site inside of the iframe so that is no use.
> I suggest that the search link on www.gromacs simply link out to google
> for now as the current search doesn't appear to work.
Good idea. I've posted this information a few times, but in case anyone's
missed it, the archive *can* still be searched from the "old" site:
Same old familiar interface :)
> In any event, the answer is here:
> -- original messsage --
> I am trying to solvate a peptide which has an acetylated N-terminus in the
> opls-aa force field. Running pdb2gmx (v. 4.0.2) gives me the following
> Error 1
> No default Ryckaert-Bell types.
> The guilty atoms in the topology are 4 atoms at the N-terminus. This issue
> has been raised before as well in the mailing lists.
> Is there a way to fix this?
> thank you
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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