RE: AMBER: NAD parameters

From: Ross Walker <>
Date: Tue, 24 Apr 2007 12:32:27 -0700

Hi Jardas,

> I am trying to use the parameters developed for NAD by Ross Walker,
> downloaded from
> However, when I load all the files in leap, the hydrogens are
> not added
> correctly to the NAD molecule complexed with my protein.
> Does anyone have an idea of what is going wrong? Did I miss something?

I need some more information here to be able to help. What did you actually
do? - I.e. commands you carried out in Leap etc. Did Leap give you any error
messages? And what do you mean by "the hydrogens are not added correctly" -
A screen shot of the xleap edit window showing the problem and some 2-D
schematics showing the protonation you expect and the protonation you got
would be helpful.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Apr 25 2007 - 06:07:36 PDT
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