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)? regards, Jestin Mandumpal
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