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

From: David A. Case <case.scripps.edu>
Date: Thu, 17 Jul 2003 09:05:00 -0700

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 

-- 
==================================================================
David A. Case                     |  e-mail:      case.scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Jul 17 2003 - 17:53:00 PDT
Custom Search