AMBER Archive (2002)

Subject: Question about Antechamber

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Wed Sep 25 2002 - 16:37:55 CDT

Hi Amber users,

When I try to go to MM/PBSA calculation with a small molecule, As far as I understand, in order to get an appropriate energy parameter for the small molecule, I need to use antechamber. Right? In this case, Tripos-Mol2 file is an appropriate input format to antechamber, isn't it? If so, does antechamber use atom definitions in Tripos-Mol2 file? In other words, energy parameters generated by antechamber depend on atom definitions in Tripos-Mol2 file?

Thank you in advance,

Masaki Tomimoto
Sr. Scientist
Structural GenomiX Inc.