AMBER Archive (2009)

Subject: [AMBER] Targeted MD and QM/MM

From: Gabriel Urquiza (urquizagabes_at_gmail.com)
Date: Fri May 29 2009 - 15:09:31 CDT

Dear AMBER users,

I'm pretty new in this AMBER business, and pretty interested in doing a
Targeted MD of a new ligand in the active site of Farnesyl Pyrophosphate
Synthase (1YHL). I'm following exactly the Efavirenz tutorial to build the
topology of our ligands and I'm not being exactly successful. The problem is
that the atom types for my ligand A0N can't be determined, and so I can't
build my topology and coordinate files for the complex enzyme-ligand. I
would also like to ask if that is strictly neccessary for performing QM/MM
on the active site of the enzyme. I'm sending along the LEaP log of my last
use.

Any help regarding this issue would be kindly welcome. I've been struggling
with this problem for ages now and it is really depressing to get error
messages around twenty times a day. Please help.

Gabriel Urquiza
Post graduation student. Universidade Federal da Paraíba - Brazil


  • application/octet-stream attachment: leap.log

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