How do you decrease the number of solvent molecules in a topology file? I think this will solve my problem.
On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan <rajatdesi...@gmail.com>wrote: > Hi, > In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral > -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I > don't think the ions are written into your .top . Please check and see if > grompp works. > > > On Sun, Aug 25, 2013 at 9:34 AM, The One And Only <chappybo...@gmail.com > >wrote: > > > I've tried the same process twice to two different proteins, but still > got > > the same error that the #coordinates in the topology file did not match > the > > #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is > > the process I went through: > > > > *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* > > > > *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* > > > > *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* > > > > *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* > > > > *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* > > > > *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* > > > > *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname > > NA -nname CL* > > > > *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o > > 1xyw-EM-solvated.tpr* > > -- > > 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 > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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 > -- 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
