[gmx-users] RTP file formats

Justin A. Lemkul jalemkul at vt.edu
Thu May 5 14:38:55 CEST 2011

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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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