On Fri, Jun 16, 2017, Vishal Nemaysh wrote:
>
> *antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2antechamber
> -i lig.pdb -fi pdb -o lig.prepin -fo prepi *
Your ligand has a net charge of -3, so you need to use the "-nc" flag if you
are trying to get charges.
Also, you have a bad contact (0.9 Ang.) between two hydrogens...that may cause
problems.
You have no residue names in columns 18-20; hence I get this (AmberTools17):
slater% antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2
Welcome to antechamber: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
/home/case/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Residue Names must be in Columns 18-20.
This info should help you get going....good luck....dac
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Received on Fri Jun 16 2017 - 08:30:03 PDT
