AMBER Archive (2004)

Subject: Re: AMBER: averaged structure with unknown elements

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 25 2004 - 16:15:25 CST

On Wed, Feb 25, 2004, Youyi Peng wrote:
>
> After averaging a structure from the MD trajectory in PDB format, I loaded
> this structure into xleap to make top and crd files for energy
> minimization.

This sounds strange: you don't need a new prmtop file in order to do
minimization...in fact, it is generally important _not_ to change parameters
in this way.

...good luck...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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