From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Wed Dec 21 2016 - 03:02:05 CST

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.