[AMBER] Antechamber Error

From: Rana Rehan Khalid via AMBER <amber.ambermd.org>
Date: Thu, 16 Feb 2023 13:35:10 +0500

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
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