Dear Amber users,
I am trying to use antechamber to generate a prep file for the ligand
(AHD) of my protein. The problem I have come across is that when I try
to run antechamber I get this error back:
crick:~/Documents/6ggj> antechamber -i AHD.pdb -fi pdb -o AHD.prepin -fo
prepi -c bcc -at gaff
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, abcg2, and sybyl.
-- Check Format for pdb File --
Status: pass
Info: Bond types are assigned for valence state (84) with penalty (2).
Info: Total number of electrons: 234; net charge: 0
Running: /opt/amber24/bin/sqm -O -i sqm.in <http://sqm.in> -o sqm.out
/opt/amber24/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/opt/amber24/bin/sqm -O -i sqm.in <
http://sqm.in>
-o sqm.out"
Does anyone know how to solve this problem? Any help would be appreciated
Thank you,
Rosa Teijeiro
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 20 2024 - 09:00:02 PDT
