On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman <[email protected]> wrote: > Dear all, > I have generated .gro and .top file for Chloranil from prodrg > and tried solvate it using pre-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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Best Regards, lina -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
