AMBER Archive (2004)

Subject: Re: AMBER: nmode with mm/pbsa

From: Rhonda Torres (torres_at_scripps.edu)
Date: Thu Jun 10 2004 - 13:33:40 CDT

Hi Nan,

See p. 215 of the Amber 8 manual. It describes how the stripwater (and
ptraj) and (or) writeparm commands can be used to create a prmtop file
corresponding to the modifications you would like to perform.

Hope this helps.

Rhonda

On Wed, 9 Jun 2004, Nan Lin wrote:

> Hi,
>
> I am trying to calculate entropy by nmode through mm/pbsa.
What I want to do is to cut a 8 A sphere around the ligand ( it's a complex
with protein and ligand) from the MD snapshot. I used carnal to do that.
But I also need a corresponding topology file with atoms only in 8 A range.
How can I do that? I checked rdparm, but don't know how to do that.
I also tried recreating topology file by tleap. But it didn't work
since tleap add extra hydrogens after the original bond between residues
have been broken. Please let me know if you have any suggestions or solutions.
>
> Your help is highly appreciated!
>
> Nan
>
>
> ---------------------------------
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