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
Mob:
8017650842
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 17 2019 - 05:00:02 PDT
