You need to look in the sqm.out file to get information about the error.
...dac
On Fri, Sep 20, 2024 at 9:38 AM Teijeiro Juiz, Rosa via AMBER <
amber.ambermd.org> wrote:
> 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
>
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Received on Fri Sep 20 2024 - 09:30:03 PDT
