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

Du Jiangfeng (BIOCH) j.du at maastrichtuniversity.nl
Thu Sep 8 10:29:40 CEST 2011

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?

Any help will be appreciated,

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands

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