On Wed, 2014-09-17 at 09:28 +0530, sunita.tifrh.res.in wrote:
> Hi Jason,
>
> You are familiar with editing a topology file to a given force field type.
> Could you please provide a tutorial may be on a tripeptide or tetrapeptide
> which would be a simplified system. It will be very much useful to many
> users. Further, it will reduce the incorporation of errors in the topology
> file.
There is no hard-and-fast rule for modifying a topology file to
implement a force field. You need to have a look at the force field
definition, start with one that is close, and then use ParmEd to make
the changes necessary to implement the new force field.
The only success story I know about off the top of my head is
implementing the off-diagonal modifications to the Chen et al. RNA force
field (and, of course, the 12-6-4 potential for divalent metal ions,
which is _only_ implemented through ParmEd). There is already a ParmEd
tutorial/reference of sorts that is as close as I can get to a
"tutorial" for this type of thing (see here:
http://jswails.wikidot.com/parmed).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 06:00:05 PDT
