[gmx-users] parameters for bond types for GROMOS force field.
jmsstarlight at gmail.com
Fri Jun 8 20:01:53 CEST 2012
Does the gb_10 suitable for both bonds that I want to parametrise ?
As I've told previously I need to parametrise two different bonds
1) is the >C=C< bond wich are not in the ring. This is just double bound in
linnear sequence -C=C-.
2) is the >C=N- double bond where both atoms in the 5-m ring system
2012/6/8 Justin A. Lemkul <jalemkul at vt.edu>
> 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.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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