AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 15 2008 - 11:01:55 CDT

Hi John,

 

Yes C=C bonds will be difficult with FF99SB since there is no equivalent in
the set of amino-acids. As a first pass you could define your own atom types
and copy the c2-c2 parameters from GAFF. So you'd have a type such as C2 and
then have an frcmod with

 

C2-C2 = 589.7 1.324

 

You'd then need to define the missing angles and dihedrals as well which you
could also as a first pass adapt from the GAFF parameters. The other option
of course is to use GAFF for the CHU and CHV residues. The point a meant to
make is that what you probably want to avoid is using GAFF for all the
standard amino acid residues as well. Note, you will still have to provide
parameters for the GAFF to FF99SB boundary but you should be able to do this
by analogy between the two force fields.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Grange Hermitage
Sent: Monday, July 14, 2008 5:19 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop

 

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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