AMBER Archive (2005)

Subject: RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 23 2005 - 11:26:56 CDT

Dear Daniel,

> I'm searching for parameter files for NAD.
> Since I'm using AMBER7 I have serious problems with
> the parameter files at
> http://pharmacy.man.ac.uk/amber/.

There are several sets of parameters for NAD+ and NADH here, which ones did
you use? I suggest you use the first set which are in the form of .lib (off)
and .frcmod files by Walker et al.

Are you simulating NAD+ or NADH?

Also what specifically are the serious problems you are having with the
parameter files?
 
> Does anyone know where to get newer parameter files ?

New parameter files or new parameters?

There should be nothing wrong with those parameter files, I created them and
work fine for me and many others. If you can let me know what the problems
are I can try and help you.

As for new parameters you can check the literature there may be some
"alternative" parameters published. Note, however, that those parameters
were carefully fitted for simulating both NAD+ and NADH in the Liver Alcohol
Dehydrogenase protein. They should be transferable to different NAD+(H)
environments including (but not tested) NAD+(H) in water.

> I also tried to generate parameter files myself using
> antchamber. I mannaged to create a file but if I use it,

I would be very careful using the GAFF force field with NAD+(H) since there
is some unusual bonding, two phosphate groups as well as the nicotinamide
ring and attached amide group. The fluctuations of this group are very
tricky to get correct.

> the NAD appears two times in my model since the NAD
> is added a 2nd time as a bunch of heteroatoms.

This seems weird, I would need to see you pdb to check it. Note, if you are
simulating LADH this would be correct since it is a dimer and so contains
two NADH residues. They will both need to be called NAD in the pdb in order
for Leap to recognise them properly.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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