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

JMandumpal jesbman at rediffmail.com
Wed Nov 14 09:07:21 CET 2007


  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)?

Jestin Mandumpal
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