On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım <ahmedo...@gmail.com> wrote:
> I am simulating tip5p water. I got tip5p.gro from $GMXLIB > 1.) editconf -f tip5p.gro -o protein.pdb > 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top > > 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) > > Select the Water Model: > 1: TIP4P TIP 4-point, recommended > 2: TIP3P TIP 3-point > 3: TIP5P TIP 5-point > 4: SPC simple point charge > 5: SPC/E extended simple point charge > 6: None > > 3 (TIP5P TIP 5-point) > > 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 > 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o > protein-water.gro > 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o > protein-water.tpr > Fatal error: > number of coordinates in coordinate file (protein-water.gro, 37090) > does not match topology (protein.top, 34530) > > > What does the [molecules] directive of your .top say? In principle, most of the steps carried out above are unnecessary. You've got pure water, so the topology is easy: #include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/tip5p.itp" [ system ] water [ molecules ] SOL X ...where X is the number of water molecules. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists