[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 
> impreciseness.
OM is for charged O so that is correct. O is for carbonyl (C=O) groups.
> regards,
> marc bruning
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list