[gmx-users] parameters for bond types for GROMOS force field.
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 8 19:53:03 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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