"First we built their 3D structures in the *.pdb format using Gauss View 4.0 and Frisch et al. [30<http://www.hindawi.com/journals/chem/2013/803151/#B30>] and submitted them to energy minimization with Frisch et al. [30<http://www.hindawi.com/journals/chem/2013/803151/#B30>] using the algorithm B3LYP/3-21G with charge chelpg, in order to generate their *.out files."
What does this have to do with gromacs topologies? Dr. Vitaly V. Chaban On Mon, Sep 9, 2013 at 12:53 PM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Hi Dr, > Check that link and see the role of GaussView in GROMACS. > Thank you. > http://www.hindawi.com/journals/chem/2013/803151/ > > > On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > >> Hmmm.... >> >> GaussView is a supplement to Gaussian to prepare input files and visualize >> some (but far not all) results. Of course, it has nothing to do with >> gromacs and its topologies. >> >> Or, do I misunderstand you? >> >> >> Dr. Vitaly V. Chaban >> >> >> On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS < >> mutemibiochemis...@gmail.com> wrote: >> >> > Dear Users, >> > I am trying to run Protein-Ligand MD simulations using GROMACS. >> However, i >> > seem to be lost in building correct ligand topologies. I came across an >> > article explaining that the above mentioned softwares can be used to >> build >> > a ligand topology file that can act as a guide in allocating correct >> > charges and charge groups. Is there anyone who have used them before? If >> > you have, would you kindly help me in finding my way especially in >> > generating .out files using the GaussView. >> > >> > >> > >> > Thank you. >> > -- >> > 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 >> > > > > -- > *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