AMBER Archive (2007)

Subject: Re: AMBER: RED-vIII fails

From: Jesper Soerensen (lists_at_jsx.dk)
Date: Mon Nov 05 2007 - 10:01:21 CST

Hi Francois,

Thank you for the help so far. I have a few followup questions:

1) Do I need 4 orientations for the 2nd molecule, as it is very small?

2) I think it is the ordering of the molecules (which is 1st and which
is 2nd) that causes the error, because I had another terminal residue
fragment finish correctly, I think.

3) The attempt that finished correctly placed files in 3-directories
under a directory called "0Values", respectively directories Mol_m1,
Mol_m2 and Mol_MM2. Which of these directories contains my mol2 files
that I need to create the AMBER OFF library file?

4) Thank you for sending a link to the Leap tutorial for use of Mol2
files, I was very informative, but in it I fail to see where I go from
the Mol2 format to creating a .off file which I can then load in at a
later time. The last step of the tutorial is to save the information in
a .mol2 file, not a .off file. Did I miss something there?

Regards,
Jesper

On Tue, 2007-10-30 at 22:38 +0100, FyD wrote:
> Quoting Jesper Soerensen <lists_at_jsx.dk>:
>
> > Files are attached, I figured I'd include all the data, as the file size
> > wasn't too different.
>
> - 1st in the tutorial
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php, it is written
> in the introduction:
> "RESP was recompiled using qtol = 0.1d-5, maxq = 5000, maxlgr = 500
> and maxmol = 200"
> You are using a two molecules RESP fit; with for the 1st molecule (2
> conformations x 4 orientations) and for the 2nd molecule (1
> conformation x 4 orientations). Thus, your charge derivation start to
> complex; I would recompile RESP with the keywords provided to avoid
> additional error messages...
>
> - Then, in http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11,
> the INTER-MCC are defined between a molecule 1 & a molecule 2 (only).
> The molecule 1 being the donor of chemical group and the molecule 2
> the acceptor of chemical group. In your example, you inverted the
> molecule 1 and 2 and used the molecule 2 as a donor of chemical group.
> Try to switch the order of the molecule, and see how it works: It
> should be OK.
> I want to underline that the way INTER-MCC have been set up in
> R.E.D.-III is quite rigid. In particular, R.E.D.-III only allows to
> build molecular fragments as defined in Cieplak et al. J. Comput.
> Chem., 1995, 16, 1357-1377. We changed that in R.E.D. IV and the
> building of more complex force field topology databases is now
> possible (and the way to do it is really less rigid).
>
> - Finally, once you will have generated the Tripos mol2 file for your
> terminal fragment you might considering reading
> http://q4md-forcefieldtools.org/Tutorial/leap.php. We just put new
> versions of the LEaP files to be downloaded.
>
> Please, tell me if this solves your problem...
>
> regards, Francois
>
>
>
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