AMBER Archive (2008)

Subject: Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Mon Jul 14 2008 - 19:18:40 CDT

Hi Ross,

The bond between the CHU and CHV is the = in:
CA-CB-OG-C1-C3=C4-C2-OG-CB-CA

Could you describe an approach for defining this in FF99SB ?

thanks,
    John.

On Mon, Jul 14, 2008 at 2:05 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

>
> The non-standard residues look like amino-acid type derivatives so you
> might be better off just looking for analogues in the FF99SB force field
> that you can use as templates.
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Grange Hermitage
> *Sent:* Sunday, July 13, 2008 6:07 PM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: AmberTools1.1 (and 1.0) antechamber endless loop
>
>
>
> Hi,
>
> I am getting an endless loop with AmberTools1.1 and 1.0 installations on
> different machines. I have tested this out to 1 hour elapsed time.
> However, with AnteChamber-1.27, the command completes and does so in 8
> minutes.
>
> The command is:
>
> antechamber -fi mol2 -fo prepi -i chp3.mol2 -o chp3.prepin -j 5 -c bcc -s 2
>
> The chp3.mol2 is attached.
>
> Perhaps one of the developers could execute this in their AmberTools
> environment to see what result they get there.
>
> I have a tgz of the directory used for the run, and will send if anyone
> wants to see that.
>
> Is a different means of reporting a possible bug recommended?
>
> Thanks,
> Grange.
>
>

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