AMBER Archive (2009)

Subject: [AMBER] improper torsion problem

From: Youn Kyeung Lee (
Date: Tue Jun 16 2009 - 21:36:14 CDT


I'm running amber to see the dynamic behavior of the DNA containing
methylated cytosine.

I made mol2 file for methylated cytosine by myself, and I assigned
appropriate amber atom type.

I used ff99bsc0 force field and loaded frcmod.parmbsc0.

I did parmchk, and added some improper torsions to frcmod file that I
thought they were needed.

However, the improper torsions of methylated cytosine and guanine were
destroyed after MD simulation.

I tried to solve this problem, but I could not find any solution.

I hope the attached image file will help to understand my question.

Also, I attach the mol2 file and frcmod file for methylated cytosine.

Thank You.

Youn Kyoung @ Seoul national university

  • application/octet-stream attachment: MC.frcmod

  • chemical/x-mol2 attachment: MC.mol2

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