[gmx-users] Trimer dynamics
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 4 14:39:26 CEST 2004
On Mon, 2004-10-04 at 12:33, Marc Bruning wrote:
> dear list,
> one oxygen in a phosphate group gets the gromacs atom type OM assigned while
> using the PRODRG server to generate the topology for a ligand. since i
> understand from the manual that OM means a C=O bond i am not sure if this is
> the correct classification for this atom which should be in a P=O bond.
> because there is no specific atom type for an oxygen bound to a phosphate in
> the atom type section (5.2.1) of the gmx-manual i wonder wether i need to add
> an atom type myself or if assigning C=O instead of P=O is a negligible
OM is for charged O so that is correct. O is for carbonyl (C=O) groups.
> marc bruning
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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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