AMBER Archive (2003)

Subject: Re: question about partial charge

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Feb 18 2003 - 01:56:59 CST

Dear Sychen,
for metal ions I don't know. As for organic dimer, if the two subunits are
"reasonably similar"
you could use just one. (Provided optimizing monomer you don't get too far
from its structure in the dimer).
If the two subunits are different you should derive charges on both of them
and then do multiple conformation fitting.
(for details see, Cieplak et al, J COMPUT CHEM 16: (11) 1357-1377 NOV 1995)

Alternatively, you could make methyl- or hydrogen-capped fragments of your
molecule, optimize them, calculate ESP, fit it
and go thru antechamber and prepgen to fit the charges on open-valence
fragments.

Hope this helps.

Best regards,

  Martin

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----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem

>   I also want to do a optimization calculation with HF/6-31g* function on
>   an organic molecule with two identical structure to obtain its partial
>   charge. The initial structure is extracted from a complex structure
>   stored in PDB.
>   Unluckily, this organic molecule is too large to do optimization
>   job in Gaussian98 even though I sent this job to my server, IBMP690,
>   with 16CPU. So, is it reasonable to simply do optimization job on only
>   one structure of this dimer or just do general job without optimizaion
>   on a whole dimer in order to get its ESP for RESP fitting?
>
>   Thanks for your suggestion!
>
> Best Regards,
>
> sychen.