Re: Antechamber questions

From: Scott Shandler <>
Date: Mon, 31 Mar 2003 18:42:35 -0500 (EST)

Thanks for your response, I do have a follow-up question though. (see

On Fri, 28 Mar 2003, David A. Case wrote:

>_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/ ANTECHAMBER_MUL.MOP
>_> >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.

I checked both geometry before and after the MOPAC run and all seems to be
intact. The calculations do appear to complete, and I think I might have
a lead on which "bond types may not be correctly assigned". The "peptide"
that I am attempting to determine parameters for consists of both natural
and non-natural backbone atoms (i.e. benzene ring embedded in the
backbone) Upon inspection of the ANTECHAMBER_BCC_TYPE.AC file, the bond
records that antechamber is complaining about seem to be the ones that are
non-natural in order of occurance. Would it be safe to assume that the
warning message is simply indicating that the non-natural backbone (and
side chain) bonds that MOPAC determines are unable to be confirmed
(looked up and assigned) by Antechamber since it is not naturally occuring

BOND 7 4 5 1 N H
BOND 8 4 6 1 N C !!!
BOND 9 6 7 1 C C !!!
BOND 10 6 13 1 C C !!!
BOND 11 7 8 1 C C !!!
BOND 12 8 9 1 C C !!!
BOND 13 8 14 1 C C !!!
BOND 14 9 10 1 C O

>_> 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.

Thanks, we were due for an upgrade anyway ;)

>_..good luck...dac

Thank you for your time,

Received on Tue Apr 01 2003 - 00:53:01 PST
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