[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 14 09:41:26 CET 2007

JMandumpal wrote:
>   Friends,
>   I would like to simulate a box of water  (TIP5P model), with 258 water 
> molecules. When I tried to build up the .top, .gro and .ndx files using 
> the command pdb2gmx -p -i -n -o -f tip5p_W.pdb,
> I got an error message : input/ output error, program aborted.
> MY input structure, ie, tip5p_W.pdb contains the co ordinates for the 
> solvent box and therefore I dont need to solvate it again!!
> Could you suggest the exact way to build up thes files ( .top, .gro, 
> .ndx, .itp ) with a starting structure (.pdb files)?
there are starting structures and topology in your share/gromacs/top dir.

> regards,
> Jestin Mandumpal
> ------------------------------------------------------------------------
> _______________________________________________
> 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

More information about the gromacs.org_gmx-users mailing list