[gmx-users] RTP file formats
Mr Bernard Ramos
bgrquantum at yahoo.com
Thu May 5 14:42:55 CEST 2011
Thanks for the response. We will be using the CHARMM ff.
--- On Thu, 5/5/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] RTP file formats
To: "Discussion list for GROMACS users" <gmx-users at 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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