On Thu, Apr 14, 2011 at 9:30 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Apr 14, 2011, Jason Swails wrote:
>
> > Based on your test.pdb, I'm actually surprised that it ever worked. The
> > hydrogens all have weird names that don't conform to the PDB standards
> >
> > (2HB, 3HB, 1HG2, etc.) where they should be (HB2, HB3, HG12, etc.)
>
> These are not "weird" names, they just correspond to PDB version 2, rather
> than the (current) version 3 standard. LEaP and other amber tools should
> accept the older format just fine.
>
I was wondering if this was the case. However, I didn't see anything that
would map those atoms to one another in leaprc.ff03.r1 or leaprc.ff03 (I'm
supposed to be looking for addPdbAtomMap?). It wasn't obvious to me that
leap should be able to make that connection based on what I saw in the
lib/leaprc files...
All the best,
Jason
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 14 2011 - 10:30:03 PDT
