[AMBER] Re: ligand exchange

From: John S <s.john634.gmail.com>
Date: Tue, 6 Apr 2010 04:35:39 -0400

Dear Amber Users,

While using antechamber for partial charge generation using Mulliken charge
.Is it alright if I use fractional net charge .
Does antechamber recognize fractional charges as net charge .


On Mon, Apr 5, 2010 at 6:05 PM, John S <s.john634.gmail.com> wrote:

> 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 .
> Thanks
> John
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Received on Tue Apr 06 2010 - 02:00:02 PDT
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