Subject: Re: CCL:basis set optimiser in solid

From: David Case <[email-masked]>
Date: Fri, 12 Jan 2001 09:07:25 -0800

On Thu, Jan 11, 2001, xin_hu wrote:

> Can I
> load a pdb file of protein,  assign the residues with charges, 
> and save the file as pdb or other type formate? if can, what's 
> kind of charge it is assigned? 

The standard libraries have alternate charge states (protonated and
unprotonated) for his, glu and asp.  You could make others and add to
the library, or manually modify charges using a spread-sheet like interface.
The file can be saved as PDB or Amber format.  All of this is done in
LEaP, which has an on-line manual, a printed Users' Guide and a tutorial
section.

> How to just add polar hydrogen (united atom) to residues, and how to 
> assign the kollman united atom charges using AMBER6.0?

Run xleap -s (to ignore the default startup file), then type 
"source leaprc.ff91".  This will load in the "parm91" (Weiner et al. united
atom force field).  Because this force field is so old (developed in
1983-84) it is not used much anymore; be sure this is what you really want
before spending a lot of time at it.  Amber6 is really designed with more
recent force fields in mind.

...good luck...dac

-- 

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David A. Case                     |  e-mail:      [email-masked]
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