[AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP

From: Aron Broom <broomsday.gmail.com>
Date: Tue, 16 Oct 2012 12:59:55 -0400

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

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.



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
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