[gmx-users] parameters for bond types for GROMOS force field.

[Justin A. Lemkul]

On 6/8/12 1:22 PM, James Starlight wrote:
> I've found that information in ffbonded.itp but I'm not sure about exactly
> meaning of some types.
>
>
> E.g I'm looking for bond type for simple double bond between C=C as well as C=N
> ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one
> #define gb_15       0.1390  8.6600e+06
> ; CH2  -  C, CR1 (6-ring)       800
>
>    and for the second one ;
>
> #define gb_11       0.1340  1.0500e+07
> ; C  -  N, NZ, NE       900
> ?
>

Neither.  gb_10 sounds exactly like what you need:

#define gb_10       0.1330  1.1800e+07
; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)       1000

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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