On Tue, Oct 4, 2011 at 2:13 PM, Peter Eastman <peastman.stanford.edu> wrote:
> Thank you!
>
> > Just out of curiosity, did you use
> http://ambermd.org/doc/OFF_file_format.txt? If so, did you see any
> glaring mistakes in it, or did you find it helpful at all?
>
> Yes, no, yes in that order. :) I did find some bugs in the
> all_aminont94.lib file, though. For the ACE group, the residueconnect
> section says
>
> 1 5 0 0 0 0
>
>
> which claims that atom 1 (one of the hydrogens in the CH3 group) will be
> bonded to an atom in another residue. The NME and NHE groups have similar
> problems. We reported this to David Case, and he said he didn't think the
> residueconnect section was ever used. Still, it would be very helpful to
> either 1) fix this problem, or 2) indicate in the documentation that the
> residueconnect section is deprecated, contains errors, and should not be
> used.
>
Ah. I had no idea that the residueconnect sections weren't used anymore. I
also didn't know there were any mistakes in it since my sample size for
determining if they were accurate was checking CYX (it had 3 connections on
there -- head, tail, and disulfide), and a bunch of the N-termini and
C-termini. The only ones that are "broken" are the caps (and I found the
reason why). It's been fixed for the next version of AmberTools release
(I'm not sure if this along with the previous issue you found qualifies for
a full bugfix in the current AmberTools, but if it does I'll post it).
All the best,
Jason
> Peter
>
>
> On Oct 4, 2011, at 10:34 AM, Jason Swails wrote:
>
> > In that case, see the attached file. I checked the diff log and the only
> > thing that changed after re-running the ff10.cmd file were the atomic
> > numbers. I had to rename the file extension .txt or else gmail wouldn't
> > allow me to send the file.
> >
> > Just out of curiosity, did you use
> > http://ambermd.org/doc/OFF_file_format.txt? If so, did you see any
> glaring
> > mistakes in it, or did you find it helpful at all?
> >
> > Thanks!
> > Jason
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 14:00:04 PDT
