if you prepare a separate ITP for each solvent, you will save some nerves in the long term....
Dr. Vitaly V. Chaban On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/11/13 8:59 AM, Shima Arasteh wrote: > >> Dear all, >> >> I see cyclohexane parameters in top & par CGenFF files. Would it be >> correct if I add this molecule to the rtp file in charmm and then use it as >> a solvent rather than for example water? >> > > The .rtp mechanism is generally used for building blocks of larger > molecules, for which topologies are built with pdb2gmx. There's nothing > wrong with building an .rtp, but it's probably about the same work as > building an .itp, and then you have to run pdb2gmx and modify the topology > it gives you (from .top to .itp). Save some work and just write the .itp > file, especially since you already have all the parameters. > > Generally, how is it possible to add a new solvent to the charmm ff >> simulations? >> >> > Like you would any other standalone molecule - write an .itp for it. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > 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