AMBER Archive (2007)

Subject: Re: AMBER: RED-vIII fails

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 05 2007 - 12:27:33 CST

Quoting Jesper Soerensen <lists_at_jsx.dk>:

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

Up to you...
- You control molecular orientation using RBRA: This is a 1st good point.
- Then, you apply multi-orientation, this a second good point.
Then , you might read:
http://q4md-forcefieldtools.org/RED/FAQ-III.php#6

> 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.

Thanks, for pointing this to our attention. We are working on this
problem to try to make R.E.D.-III "less rigid": It is not normal it
works in one order and not in the other one... I let you know if we
solve this problem. However, the answer to the problem your reported
is definitively R.E.D.-IV...

> 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?

Mol_m1 this is a single molecule (molecule 1) fit
Mol_m2 this is a single molecule (molecule 2) fit
Mol_MM2 this is a multi-molecule fit: in your case, you get the
fragment you are interested in.

> 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?

TEST = loadmol2 Mol2file-from-RED.mol2

APPLY THE TUTORIAL @
http://q4md-forcefieldtools.org/Tutorial/leap.php

savemol2 TEST New-Mol2file.mol2 0
(or savemol2 TEST New-Mol2file.mol2 1)
=> fragment coordinates more correct (for R.E.DD.B. for instance)

saveoff TEST Your-name.off
=> for AMBER simulation

regards, Francois

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