AMBER Archive (2002)

Subject: MM-PBSA basics

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Fri Sep 27 2002 - 14:53:01 CDT

Hello,

I am attempting to get started with MM-GBSA on a protein-ligand
complex. There are 136 (non-water) residues in my trajectory, with
residues 1-133 being protein and 134-136 being ligand.

I *really* have read the manual, looked at the examples, and scoured the
e-mail reflector, but still am unclear on some basics. I want to get
the decomposed free energy components of the ligand-protein
interactions. I want to use just the trajectory (not 3 separate
topology files, if possible).

1) COMREC, RECRES etc.: This is clear as beer in the input file, but
I'm still unsure if I've got it right.
I'm assuming that, because I'm not giving 3 topology files, the
numbering scheme is as follows:

COMREC 1-133
COMLIG 134-136
COMPRI 134-136
RECRES 1-133
RECPRI 1-133
RECMAP 1-133
LIGRES 134-136
LIGPRI 134-136
LIGMAP 134-136

2) Makecrd - this is where I define ligand/receptor if using a single
trajectory? In other words, do I need to define lstart, lstop, rstart
and rstop if I've already done so as seen above?

Thanks much,

Michael Ford