Dear Amber Experts
I am facing the problem of parameterizing a ligand. Here is the command I
use
antechamber -fi pdb -fo mol2 -i test.pdb -o lig.am1bcc.mol2 -c acc -pf y
-nc 0
It shows the error
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag
are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
Status: pass
Info: Determining atomic numbers from atomic symbols which are case
sensitive.
/home/rehan/Downloads/amber22/amber22/bin/wrapped_progs/antechamber: Fatal
Error!
Please guide, How I can resolve this issue. The program is complaining
about the fluorine atom (FAA), however F atom type is not an unknown atom
type for Antechamber. I am also attaching the ligand file.
Best
Rehan
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Received on Thu Feb 16 2023 - 01:00:03 PST
