Find out why your charge is not integral! Read all the output of whatever tool built the .itp file and reconsider your choices.
Mark On Mon, Sep 9, 2013 at 9:46 AM, MUSYOKA THOMMAS <mutemibiochemis...@gmail.com> wrote: > Dear Users, > I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried > to build topology files of my ligands using external tools like PRODRG > server. I tried to correct the charges in line with Dr. Justin's paper > *Practical > Considerations for Building GROMOS-Compatible Small-Molecule Topologies, *but > seems i cannot find the way, as the system crashes down during the > solvating stage > with an error message;* the net charge of my structure is not an integer > value. * > > I will be glad to get any assistance. > > Thank you. > > -- > *MUSYOKA THOMMAS MUTEMI > Mob nos **+27844846540** > B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science > (Nagasaki University)* > *PhD Student-Bioinformatics (Rhodes University) > *Skype ID- MUSYOKA THOMMAS MUTEMI > Alternative email - thom...@sia.co.ke > * > > "Do all the good you can, > By all the means you can, > In all the ways you can, > In all the places you can, > At all the times you can, > To all the people you can, > As long as ever you can." > > - John Wesley. > * > -- > 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
