Dear Francois,
> I do not know which version you use.
Thanks for the help. The version I'm using is III.2.
> However, in the case of such cofactors - with
> negative charge(s) - it is unlikely the structure after
> optimization will be similar to the that taken from the
> X-ray structure.
That's why I thing it's even more reasonable to use that conformation. Don't you?
> So you need to find a way to solve this problem...
Maybe the ideal would be to use some method like ONIOM..?(what you be far from my wishes...rsrsrs!)
>I can send you the corresponding force field libraries in the
>Tripos mol2 file format to your personal email address if you tell me the
>cofactor(s) you need, their total charge as well as the force field you >plan to use.
If I understood your notation the (P"-2") means the charge on phosphate group(s) equal to -2 (not the total charge). So, I'd be grateful if you send me the following files with Hornack et al. force fields.
NAD (P"-2")
NADH (P"-2")
NADP (P"-2")
NADPH (P"-2")
FMN (P"-2")
FMNH (P"-2")
Thanks in advance.
Josmar Rocha
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Received on Wed May 20 2009 - 15:20:42 PDT
