Thanks for the response. We will be using the CHARMM ff.
--- On Thu, 5/5/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] RTP file formats To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Thursday, May 5, 2011, 8:38 PM Mr Bernard Ramos wrote: > Hi everyone! > The *.rtp file formats we have on Gromacs rtp file exmaples do not >necessarily have the [dihedrals] or [impropers] part. They normally only have >the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the >constants or parameters. This is not what is written or Different force fields work in different ways. Gromos, for instance, uses #define statements to replace listed gb_*, ga_*, etc. > shown as an example in the manual. Is is ok to just enumerate or list The manual shows a generic example, which may not be the same for all force fields. > down the [atoms] and [bonds] but not including the rest? Thanks. > Per the example in section 5.6.1, only the [bondedtypes] and [atoms] directives are mandatory, but in the case of a bonded molecule, I believe [bonds] are as well. The rest of the directives, if not otherwise specified, are constructed from the existing information. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
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