[AMBER] Suggestion about proper ANTECHAMBER usage

From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Date: Fri, 17 May 2019 17:08:52 +0530

Respected All,
I am trying to parameterize a lipid ligand using ANTECHAMBER and I am
following the SUSTIVA tutorial.
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?

Looking forward to hearing from you.

With regards,
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
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Received on Fri May 17 2019 - 05:00:02 PDT
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