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 <atul44_sit.jnu.ac.in>:
> 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
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 422; net charge: -4
>
> Running: /home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in
> -o sqm.out" of bcc() in charge.c properly, exit
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Sat Aug 20 2016 - 02:30:03 PDT
