Re: [AMBER] Suggestion about proper ANTECHAMBER usage

From: David A Case <>
Date: Fri, 17 May 2019 09:25:17 -0400

On Fri, May 17, 2019, Saikat Dutta chowdhury wrote:

>I have isolated the lipid coordinates from the original pdb and used
>avogadro to add hydrogens. The charge of the lipid head group is -1.
>I am using the following command for parameterization.
>antechamber -i paA-new.pdb -fi pdb -o paA.mol2 -fo mol2 -c bcc -s 2 -at
>gaff2 -nc -1
>My question is whether I am doing it correctly as I am using the "-nc" flag
>with -1?

Looks OK to me: if the charge of "paA" is -1, then you need the nc flag
you use above.


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Received on Fri May 17 2019 - 06:30:08 PDT
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