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

[James Starlight]

Justin,

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

Thanks again,

James



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
>
> --
> ==============================**==========
>
> 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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