On Tue, Sep 25, 2012 at 11:57 AM, Nur Syafiqah Abdul Ghani < pqah...@gmail.com> wrote:
> Dear All, > > I already produce my co-solvent topology file also with gro file. > Next step is i need to put the co-solvent first before i enter the > water molecule inside my box and mix them with the protein. > But right now i had a problem during put the co-solvent part. > > I used this command : genbox -cp protein_box.gro -ci solv.gro -p > control.top -o protein_solv.gro > > but then there was no any molecule of my co-solvent inside the box > with the protein. > Then i know i must have the itp file to include in the control topology. > But what i can do with the topology of the co-solvent?What is the > relationship between co-solvent.gro and > co-solvent.top which i might can used both of them in my GROMACS > simulation? > > Four your infomation i used antechamber to produced my co-solvent topology. > Any advises from the pro one? > > Thanks in advance! > > -- > Best Regards, > > Nur Syafiqah Abdul Ghani, > Theoretical and Computational Chemistry Laboratory, > Department of Chemistry, > Faculty of Science, > Universiti Putra Malaysia, > 43400 Serdang, > Selangor. > 013-7188131 > alternative email : syafiqahabdulgh...@gmail.com > -- > 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 > Dear user you need to determine the number of co-solvent molecule in genbox command with -nmol option. -- masumeh -- 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