dear timo Please send me further details. I'm not a professional. Thanks and regards
On Thursday, November 28, 2013 4:28 PM, Timo Graen <tgr...@gwdg.de> wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: > Hi GMX Users, please help me > I am trying to begin a simulation of a protein and ligand coplex by > gromacs4.6.3. > > I am using AMBER99sb-ILDN force field and TIP4P water model. However, > I am facing a problem in the ion adding step. > > when I issue the grompp command to generate the necessary .tpr file > for simulation to be utilised by genion tool, I get the following > error : > > Fatal error: > number of coordinates in coordinate file (solv.gro, 102546) > does not match topology (topol.top, 133916) > > whe i use tip3p, i don't get error. > > Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.