AMBER Archive (2004)

Subject: Re: AMBER: Problem : antechamber produces no output

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed May 12 2004 - 09:40:00 CDT

Hi, Marc,
The output format, gcart is not correct. It should be "-fo gcrt".

Best

Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

owner-amber_at_scripps.edu wrote on 05/11/2004 05:19:52 AM:

> Dear AMBER users,

> I found a problem running the following command :

> shell% antechamber -i h2po4fin.pdb -fi pdb -o test.out -fo gcart

> It immediately finishes and produces no output (test.out) nor any error
> messages on the terminal.

> Does anybody had the same or similar problem before ?

> Can somebody please give me some advice on which could be the problem
> and/or how to track it down ?

> My amber version is 7, I compiled it using g77 in a linux 2.4 machine
> (IA32)

> The input file is the below one :

> HEADER
> REMARK Title Card Required
> HETATM 1 P 1 -0.075 0.121 0.069 P
> HETATM 2 O 1 -0.171 0.129 1.541 O
> HETATM 3 O 1 1.492 -0.025 -0.362 O
> HETATM 4 O 1 -0.638 1.172 -0.800 O
> HETATM 5 O 1 -0.649 -1.330 -0.410 O
> HETATM 6 H 1 -0.829 -1.894 0.352 H
> HETATM 7 H 1 1.685 0.516 -1.137 H
> CONECT 1 2 3 4 5
> CONECT 2 1
> CONECT 3 1 7
> CONECT 4 1
> CONECT 5 1 6
> CONECT 6 5
> CONECT 7 3
> END

> Regards,
> Marc

> --
> Marc Perea - Systems Administrator
> Computational Medicine Laboratory, Bioestatistics Dept.
> Universitat Autonoma de Barcelona, http://lmc.uab.es
> Tel : (+34) 93 581 38 12
> Fax : (+34) 93 581 23 44
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