Hi Francois,
I looked through the tutorial, but still not sure about which set of atoms
to select for REORIENT, although I can get a vague idea from
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
I looked at the leap script provided and still not clear. So after I got
RESP charges for the thio sugar, how do I set other parameters since it is
not a standard module in any force field? Use antechamber with GAFF force
field? Manually create a .frcmod file?
Especially how to specify bond, angle, dihedral parameters for the linkage
once I linked this thio sugar with another standard sugar (with GLYCAM
parameters)? Adding something in the building block as GLYCAM and 99SB do?
Thanks again!
Yun
On Thu, Aug 25, 2011 at 11:56 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 18:30:04 PDT
