AMBER Archive (2003)

Subject: Re: Antechamber questions

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 28 2003 - 13:58:00 CST

On Thu, Mar 27, 2003, Scott Shandler wrote:
>
>
> 1) I am running Amber 7 with Mopac 7 and have linked the appropriate
> files so that I can finally get output file, however I get the following
> message:
>
> >~/work/seq/test ->antechamber -i hetero_antechamber.pdb -fi pdb -o
> >hetero.prepin -fo prepin -c bcc
> >
> >Running: /usr/local/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
> >ANTECHAMBER_MUL.OUT
> >Mopac job ANTECHAMBER_MUL.MOP started
> >Mopac job ANTECHAMBER_MUL.MOP has finished
> >
> >Warning, 45 bond types may not be correctly assigned

sounds bad...does your molecule have a good geometry (before, but especially
after) the MOPAC run? Does the output from mopac look good...check for
any indications of failures.

>
> 2) I am attempting to generate molecular fragment parameters with Amber 7,
> and was wondering if there is any way to generate backward compatible
> united atom parameters?

No, we have not done anything on the united atom front for many years.

..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
==================================================================