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

[David van der Spoel]

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.
h2po4.itp

> 
> Generating a sensible topology is much harder than generating a starting 
> structure.
> 
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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