> On Sun, Sep 14, 2014 at 7:46 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > It can be tricky to get everything correct. The 2009 Best/Hummer
> > modifications involve only corrections to the psi angle, but you have to
> > make sure that they are not applied to glycine or proline. I'm not sure
> > that this can be done inside tleap without making some new atom types that
> > are specific to GLY and PRO. This might be a place where a ParmEd script
> > could be of real use.
I figured if I mentioned ParmEd, that Jason would have had a solution by
now. :-) Of course, as others have mentioned, the problem is not so much
doing this (you could even hand-edit your ff99SB-ildn prmtop file to make it
ff99SB*-ildn), as in making sure it agreed with GROMACS, or whatever other
program (desmond?) provides the "reference implementation" for ff99SB*-ildn.
Force field interoperability has made significant strides recently, mostly by
programs that manipulate "low-level" descriptions like prmtop, PSF or tinker
analyze files. There are lots of Google hits (including at the Amber web
page) for programs to convert Amber topologies to Gromacs, but I'm not
personally aware of work in the other direction. (Pipe up if you know how to
do this). That sort of tool would enable users to build the system in
Gromacs, then run it in Amber.
...dac
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Received on Tue Sep 16 2014 - 13:30:02 PDT
