Dear Dilraj,
If you read the LEaP script in the F-90 R.E.DD.B. project, the 'OS'
atom type is used.
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
However, this is highly related to recomputing or not recomputing new
FF parameters and defining a new atom type...
In F-90 GAFF is not used, but Amber99SB is used...
('os' in GAFF = 'OS' in Amber99SB)
regards, Francois
> Please excuse me if this has been discussed before
> in the mailing list. I could not come across a very satisfactory
> conclusion and hence am posting this in the list to get your feedback.
>
> I am currently setting up a system for simulation which a ligand
> molecule consisting of a tri-phosphate group similar to ATP and GTP. I
> used the antechamber from Amber11 and looked into the atom type
> definition for the ligand atoms. For the atoms bound to the phosphate,
> they are defined as either "o" or "os".
>
> If I look at the gaff atom force field definition,
> o-sp2 oxygen in C=O, COO-
> os-sp3 oxygen in ethers and esters
>
> Now I am fine with the hybridisation state definition of the atoms and
> hence the corresponding atom type definition in my ligand.
>
> However, I was wandering if this is the current state of atom-type
> definition for the phosphate bound atoms in the GAFF parameters? And
> if this is a reasonable definition for our calculations.
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Received on Mon Jun 18 2012 - 05:30:04 PDT
