I did as you instructed however then I seperated them into monomer and run with antechamber it appears error, and the total net charge is 0
antechamber -i phenol.pdb -fi pdb -o phenol.mol2 -o mol2 -c bcc -s 2 -nc 0
Number of electrons is odd
How should I proceed?
min
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: jun kit <klorin2002.yahoo.co.uk>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 22 November 2011, 0:50
Subject: Re: [AMBER] help with antechamber
On Sun, Nov 20, 2011, jun kit wrote:
> So, you mean I should derive the charge of the individual amine molecule
> and phenol molecule independently? After that using TER card at pdb for
> them individually too because they are not bonded?
Yes....dac
>
> Second, for the LIG, take just *one* residue (of each chemical type) and
> give it to antechamber; then load the library and frcmod files you get
> into LEaP, finally using loadPdb to read in an edited version of your pdb
> file. (Editing: make the water atoms and residues have proper names; put
> a TER card between each individual molecule.)
>
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Received on Tue Nov 22 2011 - 14:30:02 PST
