AMBER Archive (2003)

Subject: Re: Antechamber

From: Shweta Sikri (ssikri_at_wesleyan.edu)
Date: Wed Jun 25 2003 - 14:26:31 CDT

Hi,
Thanks for prompt response. Actually, I tried a small database set, but it
just assigned charges to first molecule in the database. For your knowledge
I''m using the antechanber command like this:
antechamber -i input -fi format -o output -fo mol2 -c gas
I tried with "mdl" and "mol2" input file formats, but didn't work.
For database am I need to use any other command or need to use any script file?
Also I was just wondering that what "-cf " stands for in antechamber command?
Thanks,
Shweta

At 10:31 AM 6/25/2003 -0700, you wrote:
>On Wed, Jun 25, 2003, Shweta Sikri wrote:
>
> > I'm using Antechamber for assigning charges to organic molecules. I was
> > just wondering that if it can assign charges for small molecule database
> > like CSD etc.
>
>If you limit the selection to organic molecules, it should work. Over
>large databases, you will find that a small percentage will not get good
>bond types. For these, am1-bcc charges will fail, but you should still
>be able to generate RESP charges.
>
>..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
>==================================================================