[gmx-users] TIP5P/TIP4P and OPLS-AA

[John R. Dowdle]

I am trying to set up my system with the OPLS-AA force-field and TIP5P water
model.  After generating the cubic box and adding solvent with editconf and
genbox, the resulting .gro file does not include the coordinates of the lone
pairs.  This leads to the following error in grompp:

Fatal error:
number of coordinates in coordinate file (prot_wat-b4em.gro, 9000)
             does not match topology (prot_wat.top, 14816)

The missing coordinates are of course the lone pairs on each of my 2908 water
molecules.

I have tried the same setup with TIP4P, and I encounter the same problem.

I have searched the email archives and found similar problems, but I was unable
to find a solution.

Could someone please let me know what I'm doing wrong?

Thanks in advance,

John