Dear Josmar,
>> 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?
Yes, why not. Try & See... However, the X-ray resolution of the
structure containing the co-factor might become a limitation. This is
why we always use QM geometry optimization as a _general_ method to
try to generate "canonical" building blocks.
>> 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!)
In Oniom or implicite solvent conditions you consider your co-factor
as a whole molecule; I see two main limitations (i) how efficient will
be the Oniom or the implicite solvent method in reproducing the
environment and (ii) the size of some co-factors.
This is why we use the building block approach described by Cieplak et
al. Application of the multimolecule and multiconformational RESP
methodology to biopolymers: Charge derivation for DNA, RNA, and
proteins. J. Comput. Chem. 1995, 16, 1357-1377.
The main limitation here is to find the correct connecting groups. The
main advantage is that you can handle large number of co-factors in
the same approach (and built the corresponding force field topology
database).
See
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#22
Moreover, using R.E.D. derived charge values are always reproducible.
>> 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.
Hornak et al. Sorry for him. My mistake ;-)
> NAD (P"-2")
> NADH (P"-2")
> NADP (P"-2")
> NADPH (P"-2")
> FMN (P"-2")
> FMNH (P"-2")
I send you the 6 force field libraries in the Tripos mol2 file format
to your personal address. If you compare these 6 files and the
different residues present in the files, the building block approach
will become obvious.
regards, Francois
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Received on Wed May 20 2009 - 15:25:40 PDT
