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From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Wed Dec 21 2016 - 03:02:05 CST
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Hi all,
I am facing a problem in determining the number of periodicity for ffTK dihedral parameter optimization. Currently, I am working with a pyruvated beta-D-mannose. Prior to the optimization with ffTK, I have used CGenFF program to identify the entities that have high penalties and need further validation/optimization. Based on the output of CGenFF, the following needs further validation/optimization. Could anyone in the VMD group can shed some light to determine periodicity and phase shift for the following?
dihedral {CC3161 OC301 CC301 CC2O2}
dihedral {CC3161 OC301 CC301 CC331}
dihedral {CC3161 OC301 CC301 OC301}
dihedral {CC321 OC301 CC301 CC2O2}
dihedral {CC321 OC301 CC301 CC331}
dihedral {CC321 OC301 CC301 OC301}
dihedral {CC331 CC301 CC2O2 OC2D1}
dihedral {CC331 CC301 CC2O2 OC311}
dihedral {OC301 CC301 CC2O2 OC2D1}
dihedral {OC301 CC301 CC2O2 OC311}
Thank you.
Best Regards,
Ernest
PhD candidate in Mechanical Engineering
School of Engineering and Information Technology (SEIT)
University of New South Wales, Australia.
- Next message: Chris Neale: "trajectory smoothing with periodic images in VMD"
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- Reply: Vermaas, Joshua: "Re: How to determine periodicity and phase shift for ffTK dihedral parameter optimization?"
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