AMBER Archive (2004)

Subject: Re: AMBER: antechamber

From: David A. Case (case_at_scripps.edu)
Date: Sat May 15 2004 - 11:02:30 CDT

On Sat, May 15, 2004, anshul_at_imtech.res.in wrote:

> I am facing some problems while using antechamber in amber7 to generate
> charges and atomtypes for a molecule. everytime i run it using mopac 7 it
> gives me this message
>
> antechamber -i atra+lys_min.pdb -fi pdb -o atra.prepin -fo prepi -c bcc
> Running: /home/users/harpreet/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
> ANTECHAMBER_MUL.OUT
> Unable to find mopac charges in ANTECHAMBER_MUL.OUT
> but it the ANTECHAMBER_MUL.OUT file is always empty, it does not write
> anything in it.

>
> I am attaching th einput pdb file with this mail.
>

> !BIOSYM archive 3
> PBC=OFF
>
> !DATE Sat May 15 09:13:54 2004
> C1 2.025453568 -3.786958218 7.885409832 y 1 cp C 0.248

You told antechamber that you were giving it a pdb file, but you actually
gave it a BIOSYM archive file. Since antehcamber didn't find any ATOM
records, it thought there were no atoms in the molecule.

Take a look at the ANTECHAMBER_MUL.MOP file: this is the input to mopac. You
have to get that correct first.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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