AMBER Archive (2005)

Subject: AMBER: structures extracted from mmpbsa

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Fri Aug 19 2005 - 18:25:44 CDT

Dear Amber users,

    I am studying the tutorials in mmpbsa. When I look at those structures extracted from the trajectory file under the directory amber8/src/mm_pbsa/Examples/01_GenerateSnapshots, each of the snapshot extracted looks distorted. I am wondering what causes this distortion and whether this structural distortion would affect all the energy calculations such as BOND, ANGLE, DIHED, and electrostatics.

    Another question is why idecomp only works with minimization and not with normal md. Why is minimization necessary to obtain residue energy decomposition on a structure of interest.

Thanks,
ThuZar

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