It is unclear what you want to do. The PDB file does not have this
information anywhere in its specification, so there is no Amber program
that will add it.
You can look through the parameter files ($AMBERHOME/dat/leap/parm) to see
what they are, but unless you build a topology file and analyze it (using,
e.g., parmed), there's no other way to get this information.
HTH,
Jason
On Fri, Jun 8, 2012 at 7:45 AM, Acoot Brett <acootbrett.yahoo.com> wrote:
> Dear All,
>
> Will you please tell me by which Amber command I can add partial charge,
> charge radius (van der walls radius) and charge epsilon to my protein PDB
> file?
>
> Cheers,
>
> Acoot
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 08 2012 - 07:00:02 PDT
