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

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 28 09:09:08 CET 2008

John R. Dowdle wrote:
> 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:

you have to solvate with the provided tip4p or tip5p boxes.
> 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
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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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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