I recently used tleap within AMBER tools version 12, to generate some
protein parameter files, using AMBER_FF12SB.
The command structure was:
> set default PBradii mbondi2
> model = loadpdb protein.pdb
> saveamberparm model protein.prmtop protein.inpcrd
Everything seemed to be working fine, but in trying to troubleshoot a
temperature problem I was having with OpenMM, I realized that some of the
glycine (CA-HA2 and CA-HA3) bonds were not being properly constrained. It
looking at the .prmtop file, it looks as though those bonds were not added
to the BONDS_INC_HYDROGEN list.
I haven't done any of the bugfixes for ambertools 12, but I don't see
anything about that listed. Is this something that anyone else has seen?
I haven't done a rigorous test to ensure it is reproducible, thought I
would see if anyone else has noted this kind of problem before. As an FYI,
the input pdb files I was using don't have hydrogens at all, so there
shouldn't have been any problem with LeAP not recognizing the atom name.
Thanks,
~Aron
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Oct 16 2012 - 10:30:03 PDT
