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
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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.
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