AMBER Archive (2003)

Subject: Antechamber questions

From: Scott Shandler (shandles_at_mail.med.upenn.edu)
Date: Thu Mar 27 2003 - 19:35:32 CST

Hello All,

I am an Amber newbie and have a couple of questions regarding Antechamber

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
>

The warning message concerns me, is there any resonable explaination for
this?

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?

Thanks for your assistance.

-Scott Shandler