[gmx-users] atom names

David spoel at xray.bmc.uu.se
Tue Jul 8 19:27:00 CEST 2003

On Tue, 2003-07-08 at 19:06, Carlos Emidio wrote:
> Hello gmxs!
> We´re trying to perform MD of polysaccharides. As the molucule we´re
> interested in has many ramifications, we joined each ramification to its
> respective monomer of the "main chain", making it "linear" (i tried to
> use specbonds to link the ramifications but i had some problems with
> it).
> As the atoms names for each residue were all the same, we sticked some
> Js and Ts in the beginning of all atom names.
> The problem is that genbox didn´t recognize them as Cs or Os, setting
> all vdw radius do 0.105 (though its atomtype was specified in .top
> file). Also, ngmx showed all atoms pink. How could I solve it? Is that a
> big deal? How can i tell  for sure if mdrun used the right vdw
> parameters? -- I already gmxdumped the tpr and it seemed alright --

mdrun does follow the topology, so no problem there. You can even give a
new default parameter to genbox to give your atoms slightly larger

for pdb2gmx the only requirement is that all atoms within a residue have
different names, usually they are numbered. Isn't there some standard
for naming atoms in sugars?

In principle pdb2gmx should work even with crosslinks (specified through
specbond.dat), if you have a good structure.

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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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