Dilraj,
I continue my email...
You reported "os-sp3 oxygen in ethers and esters":
You should not pay too much attention to the notion of sp3 or sp2
hybridization in the atom type definition... Indeed, an ester oxygen
with a sp3 hybridization is quite strange (at least from an organic
point of view), but this is normal ;-)
regards, Francois
Quoting FyD <fyd.q4md-forcefieldtools.org>:
> 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)
>
>> 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 - 07:30:03 PDT
