[gmx-users] No default Ryckaert-Bell. types error for N-terminus acetylated peptide, opls-aa force field

[Justin A. Lemkul]

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:

http://oldwww.gromacs.org/swish-e/search/search2.php

Same old familiar interface :)

-Justin

> In any event, the answer is here:
> http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/023872.html
> http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/023875.html
> 
> Chris.
> 
> -- 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:
> 
> 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
> 
> -Maria.
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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