On Wed, Sep 12, 2012 at 10:21 AM, Scott Le Grand <varelse2005.gmail.com>wrote:
> OK, I see what's going on. In C, numbering begins with 0. In FORTRAN it
> begins with 1. If add 1 to each number spouted by the C code, you will
> find you have a hydrogen attached to both a carbon and an oxygen.
>
> Sander does not catch this error. It should...
>
> Jason, did you guys fix the FORTRAN in pmemd to detect this yet?
>
Not that I know of. No residue in a standard library has such a topology,
and I didn't think antechamber would allow such weird bonds to be formed...
I wonder how this topology file was made.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 12 2012 - 09:00:04 PDT
