[AMBER] Weird error with antechamber for metal ion / MCPB tutorial

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 26 Feb 2020 17:01:03 -0500

Hi all,

I'm having a weird error with Antechamber here, and I wonder if anyone can
help find out what is going on. I'm trying to run *exactly* what is in the
MCPB tutorial here
<http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>, in the
session of the metal ion.

The error, basically, is that Antechamber doesn't seem to recognize *any*
metal. I got this first when trying to use an Iron ion (FE), but got the
same using the tutorial files. The following is using *exactly* what is on
the tutorial: (I downloaded the ZN.pdb file from here

$ cat ZN.pdb
HETATM 2032 ZN ZN A 262 -6.666 -1.692 15.446 1.00 12.06
$ antechamber -fi pdb -fo mol2 -i ZN.pdb -o ZN_pre.mol2 -at amber -pf y
Welcome to antechamber 19.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for pdb File --
   Status: pass
/opt/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Unrecognized atomic name ( ZN).

Would anyone know what I'm doing wrong?

Thanks a lot!

Gustavo Seabra.
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Received on Wed Feb 26 2020 - 14:30:02 PST
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