[gmx-users] How to make a CG topology for a modified residue?

[Mark Abraham]

On 8/09/2011 6:29 PM, Du Jiangfeng (BIOCH) wrote:
> Dear Everyone,
>
> I am going to simulate the interaction of prothrombin's Gla domain with membrane in martini force field. Here I encountered a problem: there are 10 modified GLUs in GLA domain. Martini force field can't recognize them. How should I overcome this problem?
>
> What I want to do now is to add this modified residue into martini force field, but I do not know whether it is feasible or logical? What's worse, I really don't know what is BNLN, BNKB or ANGL? Where can I get some references about this story?

Depending on the details of the modified GLU, you will need to consider 
the points made at 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, 
http://www.gromacs.org/Documentation/How-tos/Parameterization and in the 
Martini documentation.

Mark