AMBER Archive (2008)

Subject: Re: AMBER: Antechamber, net molecular charge

From: Junmei Wang (
Date: Mon Mar 10 2008 - 09:39:08 CDT

The program tries it best to read/calculate the charge information directly
from the input. However, not all the input formats provide the charge
information: gout, mopout, etc. explicitly have the net charge information;
the partial charges in mol2 format can be used to calculate the net charge;
while pdb format does not have charge information at all. Therefore, net
charge must be read in just for some formats. By the way, the net charge
specified by the -nc flag always override the read/calculate one.



On Sun, Mar 9, 2008 at 11:51 PM, gurpreet singh <> wrote:

> Respected users
> I am using version 9.0 of AMBER. My question is regarding the prep file
> generation using antechamber module in AMBER.
> How important is to use the option of (nc) net molecular charge ( in case
> of charge molecules) while using the command of antechamber to obtain the
> prepi file.
> I tried the same command with and without mentioning the net molecular
> charge option but did not find any difference in the two prep files.
> So where that difference will come? or lets say if I did not mention that
> option, is that a problem?
> Thanks
> Regards
> Gurpreet

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