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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Received on Sun Dec 16 2012 - 23:00:04 PST
