RE: AMBER: NAD parameters

From: Jardas sucuriba <>
Date: Wed, 25 Apr 2007 22:46:17 +0000


Thanks a lot. After visualizing my pdb file and the files
in leap and I found the problem: the names of heavy atoms of the NDP
molecule in my pdb file were not the same as in the NAD.lib file. So I
changed the names in the pdb file to the correct ones coming in the NAD.lib
and everything worked ok.
Now I have another question. After minimizing and running a small MD, I used
the trajectory as input to mm-pbsa to calculate the binding affinity of NAD
to the protein and I obtained a value of -74.05 kcal/mol.

# -----------------------
# =======================
ELE -57.51 0.00
VDW -73.20 0.00
INT 0.00 0.00
GAS -130.71 0.00
PBSUR -7.45 0.00
PBCAL 64.11 0.00
PBSOL 56.67 0.00
PBELE 6.60 0.00
PBTOT -74.05 0.00

Isn’t this value to much negative? Does anyone know about studies where the
binding energy of NAD to proteins is calculated with the mm-pbsa method or


>From: "Ross Walker" <>
>To: <>
>Subject: RE: AMBER: NAD parameters
>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
>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 |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

Verificador de Segurança do Windows Live OneCare: combata já vírus e outras

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 29 2007 - 06:07:13 PDT
Custom Search