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
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