AMBER Archive (2006)

Subject: AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging

From: Zu Thur Yew (yewzt_at_intern.bii-sg.org)
Date: Wed Jul 05 2006 - 12:03:13 CDT

Hi,

I'm new to Amber...would just like to clarify about the way the MM
energies are calculated and imaging.

Does energy evaluation require traj to be imaged? For example,
evaluating the energy of a protein-peptide complex and if somehow the
peptide has "left" the box....

I've seen suggestions of how 2 molecules can be brought back together,
where one first centers 1 molecule, image and then repeat for the whole
solute. How does that differ from centering and imaging the whole solute
in a single step?

Thanks!

Zt
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