AMBER Archive (2009)

Subject: Re: [AMBER] Can I use only a single point calculation to derive RESP charges?

From: Josmar R. da Rocha (bije_br_at_yahoo.com.br)
Date: Sat May 09 2009 - 10:19:07 CDT

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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