[gmx-users] Atom typing question

David spoel at xray.bmc.uu.se
Mon Sep 19 21:00:40 CEST 2005

On Mon, 2005-09-19 at 17:43 +0100, Joanne Hanna wrote:
> 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.
Yes and OA should be OS (if that still exists in that force field,
otherwise OA may be correct). Shouldn't one of the oxygens be

> Thanks
> Jo
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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