[gmx-users] RTP file formats

[Mr Bernard Ramos]

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

-- ========================================

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

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