Thanks David for the reply.
I was able to build topology file from the info given in
the top directory. In contrast to the .gro file for TIP5P box, containing 516
water molecules, given at the top directory, I need a specific box size with
exact number of water molecules (258 in 20.1* 20.1 * 20.1) in order to match
the experimental density 0.997 gm/cm3. So, I need to create the .gro file and
when I tried to create it with pdb2gmx -o tip5p.pdb, it didn't work as I
mentioned earlier!!!
How can I build up the .gro file for my water box.
regards,
Jestin
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