AMBER Archive (2004)

Subject: AMBER: can MM-PBSA be applied to Charmm format trajectory file?

From: jz7_at_duke.edu
Date: Thu Aug 19 2004 - 13:55:06 CDT

Dear all,

I wanted to estimate binding free energy for my protein-DNA system. It
seems that the MM-PBSA program under Amber can do that. But the trajectory
and other files I have are from NAMD (Charmm format). So I am wondering
can MM-PBSA still work in this case? If not, is there any other program or
method can estimate the protein-DNA binding free energy?

Thanks a lot!

Best,
Jeny
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