Thank you Jason. I will definitely look into this.
Best,
Sunita
> 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 - 09:30:02 PDT
