[AMBER] ligand exchange

From: John S <s.john634.gmail.com>
Date: Mon, 5 Apr 2010 18:05:34 -0400

Dear Amber Users,
I have some question on use of antechamber to get ESP charges (-c ESP) in a
ligand exchange reaction.

1. Can I generate the gaussian input file with antechamber using my initial
.pdb or .mol2 file .

2. It is a ligand exchange reaction with a large chemical structure reacting
with a metal porphyrin .

For example, if I represent my chemical structure as CH4 which I model
separately from my metal porphyrin .Here I need to get the partial charge
distribution of CH3 for a particular oxidation state, where the net charge
is 0.016 in ESP and 0.093 in Mulliken charges.Is there any way I can do it .

I tried to get the partial charges of CH4 with AM1-BCC charge method and
with output file format (-fo prepi) using antechamber, by default my charge
is 0 even on putting net charge (-nc 0.1).

Your suggestions are highly appreciated .

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Received on Mon Apr 05 2010 - 15:30:02 PDT
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