AMBER Archive (2008)

Subject: AMBER: Read trajectories generated by CHARMM

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Mon Apr 28 2008 - 08:06:17 CDT


Dear all,

     New user to AMBER. So I am sorry that if such a question is stupid.
Months ago I run a md simulation by CHARMM and wanted to analyze the binding free energy. But unfortunately, when calculating the entropy, the lack of memory problem is encountered due to the large size of the system.

    I noticed that by setting ismem=1 in AMBER, the memory requirement can be reduced to 1/3, which can be fulfilled by our machines.
So I want to know whether AMBER can read the trajectories generated by CHARMM?
If so, which forcefield should I use?
If not, could someone pls kindly give some suggestions on how to solve this problem?

Any suggestion is highly appreciated.
Thanks very much for the time.

----
Jeffrey

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