AMBER Archive (2007)

Subject: RE: AMBER: NAD parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 24 2007 - 14:32:27 CDT

Hi Jardas,

> I am trying to use the parameters developed for NAD by Ross Walker,
> downloaded from http://pharmacy.man.ac.uk/amber/cof/NAD_inf.html.
> 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
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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