AMBER Archive (2009)

Subject: Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag

• Previous message: Tomasio, Susana: "[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels"
• In reply to: Workalemhu Berhanu: "[AMBER] Tutorial 4 Please check the total charge and your -nc flag"
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On Tue, May 26, 2009, Workalemhu Berhanu wrote:

> Can I get an advise what to do with my molecules (it is an
> organic conjugated system which some aromatic rings) and it has a charge
> of one.

> $AMBERHOME/exe/antechamber -i N744HFC.pdb -fi pdb -o N744HFC.mol2 -fo mol2 -c bcc -s 2

If the net charge is not zero, you have to tell antechamber what it is using
the "-nc" flag.

...dac

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• Previous message: Tomasio, Susana: "[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels"
• In reply to: Workalemhu Berhanu: "[AMBER] Tutorial 4 Please check the total charge and your -nc flag"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]