[gmx-users] pdb2gmx: Adding non standard residues and molecular moieties

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 6 13:18:12 CET 2008

Mark Abraham wrote:
> Eddie Mende wrote:
>> Greetings
>> I am trying to generate a topology file, and
>> need to add the phosphate ion in my pdb
>> How to do this?
> Check out http://wiki.gromacs.org/index.php/Parameterization and maybe 
> http://wiki.gromacs.org/index.php/Exotic_Species

there is a phosphate ion topology in the share/gromacs/top directory.

> Generating a sensible topology is much harder than generating a starting 
> structure.
> Mark
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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