Re: [AMBER] Problem in charge generation through antechamber

From: FyD <>
Date: Sat, 20 Aug 2016 11:08:20 +0200

Dear Atul,

Your question is surprising and the answers you got even more...

I think you should wonder if it makes sense to compute the partial
charges of a molecule with a formal charge that equals -4! I would
look at the conformation of that optimized geomtry: it is unlikely to
correspond to that you need - I mean once you will be able to get that
optimized geometry (if you can manage that)...

Instead I would split this molecule into elementary building blocks to
'separate' these formal charges and then reassemble the whole
molecular system.

I would use RED Server Dev./PyRED for that...

regards, Francois

Quoting ATUL KUMAR <>:

> Dear Urers,
> I am using antechamber for generating atomic charges and parameters for a
> ligand(Net charge is -4) molecules by the following command:
> antechamber -i Mol_red5.pdb -fi pdb -o Mol_red5.mol2 -fo mol2 -c bcc -s 2
> -nc -4
> after funning this i am getting following error message:
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/bondtype -j full -i
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/atomtype -i
> Total number of electrons: 422; net charge: -4
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i -o sqm.out
> Error: cannot run "/home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i
> -o sqm.out" of bcc() in charge.c properly, exit

           F.-Y. Dupradeau

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Received on Sat Aug 20 2016 - 02:30:03 PDT
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