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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Aug 20 2005 - 00:53:01 PDT
