Date: Wed, 17 Jun 2009 03:36:14 +0100
Hello,
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
(image/png attachment: improper_mail.PNG)
- application/octet-stream attachment: MC.frcmod
- chemical/x-mol2 attachment: MC.mol2
- text/plain attachment: ATT00002.txt
