Look at the numbers, count the number of atoms you expect in each moleculetype, and work out what the mismatch is.
Mark On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl <knnar...@sssihl.edu.in> wrote: > Dear GMX users, > > I am trying to simulate a protein in SDS/Water box. > > 1. No problems with pdb2gmx - .gro file and .top files were generated. > /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/ > selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > > 2. Created a Cubic box using editconf > /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/ > > 3. Then solvated the system using genbox > genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o > protein_solv.gro -p topol.top > > 4. After this step I looked at the topol.top file and I found that it was > not fully updated and so I manually updated by adding no. of SDS molecules > under [ molecules ] section at the very end. Also I added #include sds.itp > whereever it was required. > In fact I followed the discussion between Justin, Mark and Anna Marabotti at > the following link: > http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html and did > everything that was suggested. > > 5. When I use grompp after the step 4 > grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr > > This is where I am getting a Fatal Error saying that the number of > Co-ordinates in protein_solv.gro do not match with the number of > co-ordinates in topol.top. > > Could you please help regarding this... Please give me your valuable > suggestions. > > With Thanks and Best Regards > > Naresh > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Error-while-simulating-Protein-in-SDS-Water-tp5011282.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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