[AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures

From: Yuqin Cai <yuqin.cai.2008.gmail.com>
Date: Tue, 1 Jun 2010 15:55:42 -0400

Dear AMBER community,

I am computing free energies for three carcinogen-containing duplexes using
MM-PBSA. By replacing the carcinogen with a hydrogen atom, i can compare the
distortion each carcinogen causes to the B-DNA duplex. Here are my

1) how to use multiple processes, especially during delphi? For an 800 atom
structure, it took me ~2 weeks to get the average free energy over 5000
snapshots. I wonder if i could make it faster.

2) how to put out the results for each snapshot during the trajectory,
instead of an overall average, so that I can do a clustering analyses?

3) how to cap the ends if i want to carry out analyses for a cropped

Many thanks,

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Received on Tue Jun 01 2010 - 13:00:04 PDT
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