Yun,
> Could you tell what the REORIENT means? What kind of atoms should be
> reoriented?
This keyword control the orientation of the optimized geometry before
MEP computation; this allows deriving reproducible RESP/ESP charge
values independently of the QM program used in the geometry
optimization step and independently of the initial orientation chosen
by the user.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#REORIENT
> And it seems that when I submit an ASP with sidechain de-prontonated, Ante
> R.E.D. does not recognize the charged sidechain, so I guess I should modify
> the CHARGE-VALUE and MULTIPLICITY-VALUE accordingly.
You always have to adapt the the CHARGE-VALUE and MULTIPLICITY-VALUE
accordingly to your case.
Please, use Ante_R.E.D. 2.0 available in R.E.D. Server instead of
Ante_R.E.D. 1.x. Indeed, only Ante_R.E.D. 2.0 deals with chemical
equivalencing in the P2N file format (chemical equivalencing is
important in your case for your aromatic cycle).
> In the end, I should use the script provided by F85 (script1.ff?) to convert
> the charged mol2 file to an OFF file, right? Since my fragments are not
> standard residues in GLYCAM or 99SB, I should load GAFF in the script?
You need to create your own LEaP script (similar to script1.ff) to
connect your fragments and generate your prmtop/prmcrd files. You do
not need to convert mol2 files into off files as both mol2 and off
file formats have the same role: a force field library file format (we
will release soon a new library file format; I can send you the web
link if you want to use it in LEaP).
regards, Francois
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Received on Fri Aug 26 2011 - 00:00:03 PDT
