[gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE

[Justin Lemkul]

On 1/16/17 12:04 AM, Subashini .K wrote:
>
> Hi,
>
>
>
> I am learning to prepare the residue topology file (.rtp file) .
>
>
> While preparing the file, what does the third and fourth column describe?
>
>
> This is the example of methane. What do the numbers -0.240 and 1 convey? Similarly 0.060 and 1?
>
>
> [ bondedtypes ]
> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
> 1 1 3 1 1 3 1 0
>
>
> ; Methane
> [ CH4 ]
> [ atoms ]
>
>
> C      opls_138    -0.240     1
>
> H1     opls_140     0.060     1
>
> H2     opls_140     0.060     1
>
> H3     opls_140     0.060     1
>
> H4     opls_140     0.060     1
>
>
>
> Please explain.
>

Have you consulted the documentation?

http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#rtp

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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