AMBER Archive (2002)

Subject: MM-PBSA: .crg file for Delphi

From: Thomas Steinbrecher (thomas.steinbrecher_at_physchem.uni-freiburg.de)
Date: Wed Dec 11 2002 - 12:08:40 CST

Dear AMBER users,

I plan to do an MM-PBSA calculation on a protein/ligand
complex I simulated with the ff99-force field.
I wonder what .crg-file for Delphi I should state in my
input script.
The AMBER manual states on p.18 that the ff99 force field
uses the partial charges from the Cornell et al. force
field (ff94) parameters.
So I thought I could use the my_amber94_delphi.crg file
provided with mm-pbsa for the partial charges of my amino
acids and just add the ligand partial charges to it.

Is this a reasonable approach or do I have to prepare my
own .crg file and if I have to, how do I do this?

My second question is this:

In the mail reflector it is stated that I have to prepare 3
different crd and prmtop files for lig, com and rec, even
if I only did one MD-simulation. Can I create this files by
just using ptraj to strip all residues but the ones
corresponding to ligand or receptor or complex?

Kind regards,

Thomas