Here, it will be helpful to use experimental information if possible.
The simplest thing for you to do is to find a structure in the PDB
that is similar to the cyclodextrin you want to model. If you can
find an exact match, you can use those starting coordinates and just
rename the atoms and residues -- but beware, doing this can be vexing
if the atoms aren't already arranged into the residues you need.
Or, you can measure the distances, angles and dihedrals in the PDB
structure and apply those in leap. I think it should be sufficient to
concern yourself only with the glycosidic linkage information.
I know there are several PDB structures that contain cyclodextrins.
They might be part of some larger complex, but unless the complex has
seriously strained the cyclodextrin, you can probably just use its
structure and ignore the other bits. A minimization and an MD should
shake out any stresses due to binding.
See what Dave said about antechamber. I think you'll be better off to
use the 4GA residues and structural info from the PDB.
On Mon, Dec 17, 2012 at 1:48 AM, deathsnake1991
<deathsnake1991.gmail.com> wrote:
> Dear AMBER users:
>
> I am new to AMBER. When using AMBER for the simulation of ã-cyclodextrin, I meet some problems.
>
> The force file I used is GLYCAM_06h.First I constitute my molecule by mol=sequence {4GA 4GA 4GA 4GA 4GA 4GA 4GA 4GA} in Leap. Then bond mol.1.O4 mol.8.C1 to loop the molecule. I think I should impose some angle or torsion of some bonds. But how should I choose which of them to be imposed? Could anyone give me some suggestions? Or do I make anything wrong in the steps above?
>
> Also I had try to make the ã-cyclodextrin from the ANTECHAMBER. It asked me to adjust atom valance penalty parameters in APS.DAT and increase PSCUTOFF in define and recompile bond type. I am curious of whether the parameter of cyclodextrin can be constructed with ANTECHAMBER or not.
>
> Thank you very much.
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Dec 17 2012 - 10:00:03 PST
