AMBER Archive (2005)

Subject: AMBER:idecomp

From: B (takahiro.kosugi_at_f0100090242.mbox.media.kyoto-u.ac.jp)
Date: Thu Jan 27 2005 - 05:22:37 CST

Hello Amber users,
 
I use sander with AMBER8 and have a question about output.
I use imin=5, igb=1, gbsa=1, idecomp=1.
Then, I got following output.
 
                    PRINT DECOMP - TOTAL ENERGIES
 
     resid |internal |vdw |eel |pol
|sas
============================================================
TDC 1 19.207 -5.091 -23.488 0.299 0.335
TDC 2 24.469 -1.950 -40.147 -35.551 0.645
TDC 3 17.823 -2.311 -25.772 10.225 0.234
  :
 
What are vdw, eel, pol and sas ?
I think vdw and eel contein internal energy.
Is that right ?
How AMBER calculate GB energy on residue basis ?
 
Thank you for your help.
 
Takahiro
 
===========================================================
Takahiro Kosugi
Department of Pharmaceutical Sciences,
Kyoto University, Japan
===========================================================

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