Hi, genbox can now modify the topology file by using genbox ... -p topol.top.
Best, Matthias Schmidt On Friday, August 5, 2011, lina <lina.lastn...@gmail.com> wrote: > On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman > <ravikumarvenkatra...@gmail.com> wrote: >> Dear all, >> I have generated .gro and .top file for Chloranil from prodrg >> and tried solvate it using p re-equilibrated cyclohexane. When i tried to >> generate the box containing solute it is not modifying the .top file and it >> shows zero solvent. >> Please help me how to solvate organic molecules that are obtainde from >> prodrg. >> >> Thank you. > > > Try: > > genbox -cp chloranil.gro -cs cyclohexane.gro -o system.gro > > > and manually modify the topol.top later. > > you may use the solvated pre-equilibrated cyclohexane as > cyclohexane.gro, so no need add water later. > > It should be no problem. >> >> -- >> 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 >> > > > > -- > Best Regards, > > lina > -- > 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 > -- Best, Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of Biochemistry University of Oxford http://sbcb.bioch.ox.ac.uk/schmidt.php
-- 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
