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

[Justin A. Lemkul]

On 6/8/12 2:01 PM, James Starlight wrote:
> 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
>

This is a better description.  The last message suggested everything was in a 
5-membered ring.  Had that been the case, my suggestion would have been right 
(see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in 
that case).

There are no linear C=C bonds in Gromos force fields by default, as such groups 
are not in proteins.  The closest you can likely come is to take a C=C bond from 
the PHE ring.  Bond lengths are simple, and are usually derived from 
spectroscopic information.  If using constraints on all bonds, the force 
constant is irrelevant since the bond is rigid.  If not using constraints, then 
you'll have to find or derive suitable parameters yourself.  Welcome to the 
inconvenient world of parameterization :)

-Justin

> Thanks again,
>
> James
>
>
>
> 2012/6/8 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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