AMBER Archive (2003)

Subject: Re: AMBER: mm_pbsa crg file

From: kbyun_at_wesleyan.edu
Date: Tue Oct 14 2003 - 09:09:35 CDT

Hi Thomas,

This indeed turned out to be the case when I printed
out the pdb from delphi. Thanks very much for your
help.

Best wishes,
Suzie Byun

Quoting Thomas Steinbrecher
<thomas.steinbrecher_at_physchem.uni-freiburg.de>:

> Hi,
>
> I had a similar problem once. I figured out that the
> following happened:
>
> The MM-PBSA script generates a pdb-file of your
molecule(s)
> for Delphi to read in. Check very carefully that the
atom
> names in this file match exactly the ones in your .crg
> file. In my case I had a molecule that contained
> ribose-carbon atoms named C5' or so and I added atoms
with
> that names to my charge file. The MM-PBSA script
however
> changed the names to C5* for reasons unknown to me.
So only
> some atoms of my ligand were found in .crg and very
odd
> charges were the result.
>
> Maybe thats your problem too...
>
> Kind regards,
>
> Thomas Steinbrecher
> Institut für physikalische Chemie
> Albertstr. 23a
> 79108 Freiburg
>

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