got it. Thanks Justin.
On Wed, Oct 23, 2013 at 4:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/23/13 4:28 PM, Dina Mirijanian wrote: > >> Hello, >> I am trying to convert a protein+ATP+water+ion system pdb into gromacs >> files. I need to use the existing water and ion coordinates. I can >> convert the protein part using pdb2gmx and grompp fine. But, I do not >> know >> how to process the solvent and ion coordinates separately and combine them >> to make the final system. Can anyone give me direction? I am new to >> gromacs... >> > > Copy and paste the coordinates into the pdb2gmx-processed coordinate file > (note that you can keep .pdb format or convert to .gro easily with > editconf). The solvent and ion topologies are #included in the > pdb2gmx-produced topology already, you just need to update the [molecules] > directive accordingly. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
