AMBER Archive (2009)

Subject: Re: [AMBER] net charge

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Jun 23 2009 - 09:34:07 CDT

On Tue, Jun 23, 2009, Vishal Maingi wrote:
>
> I am using my own residues which were made and minimized in Gaussian
> by DFT.. then using sequence commamnd Iwrote a script to make my
> macromolecule from the minimsed residue using gaff field. but when I run
> antechamber the net charge was -2 on molecule.though there was no charge
> on minimsed residue and all hydrogens are there on macromolecule.

We need more details on the phrase "when I run antechamber the net charge was
-2 on the molecule". Exactly what commands did you run? How did you decide
that the antechamber thought the net charge was -2?

Note that antechamber defaults to a net charge of 0; you have to use the -nc
flag to request a non-zero charge.

...dac

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