[gmx-users] Atom typing question

[Joanne Hanna]

Dear All.

I was wondering if someone could confirm whether I am right in assuming the following:

I have made a topology for AMP. My phosphate has 4 oxygens attached. The 'fourth' oxygen connecting the PO3 with the CH2 is an OA. The 3 'terminal' oxygens have no hydrogens bound in my strcuture. Therefore is it correct to assume that these 3 oxygens will be of OM type and not two of OA and one of OM as PRODRG suggested (it did not add any hydrogens to these atoms).

I have looked at the ATP topology of ffG43a2 force field and the corresponding tail PO3 group. Here the three 'terminal' oxygens are described as two of OM type (no hydrogen bound) and one of OA (hydrogen bound).

So after all of this waffle my question is that in this case where there is only:

   O
   l
 O-P-OA-CH2-
   l
   O

shouldn't the three oxygen atoms be of OM type.

Thanks
Jo