AMBER Archive (2003)

Subject: Re: AMBER: neutral N- and C- termini !

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 17 2003 - 11:05:00 CDT

On Wed, Jul 16, 2003, Xavier Periole wrote:
>
> I am going to use Gaussian to make QM/MM calculations where
> I'd like to use the AMBER force field for the MM part.
> The system I am interested in is a fragment of a protein for which
> I want uncharged N-termini (attached to an Arginine) and C-
> (attached to a Valine). I have been looking in the topology file of
> the C- and N-termini in the dat/leap/prep directory of the force field
> (downloaded from the Amber web site) and did not find any sign of
> C- and N-termini uncharged: -COOH and -NH2 respectively
>

I have not ever seen Amber topologies and charges built for these.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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