From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Thu Dec 22 2016 - 18:19:58 CST

Hi Josh,

Thanks for the feedback. Yes, the force-field of beta-D-mannose is available in CHARMM carbohydrate force field (par_allxx_sugar.inp, v 1.132). However, the force-field information of pyruvated beta-D-mannose is not available. So, the optimization that I am working on with ffTK is basically the linkages between a pyruvate group and beta-D-mannose, which are not available in CHARMM.

Thank you.

Best Regards,

Ernest

PhD candidate in Mechanical Engineering
School of Engineering and Information Technology (SEIT) University of New South Wales, Australia.

-----Original Message-----
From: Vermaas, Joshua [mailto:Joshua.Vermaas_at_nrel.gov]
Sent: Friday, 23 December 2016 1:50 AM
To: Ern Ong <Ern.Ong_at_student.adfa.edu.au>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: How to determine periodicity and phase shift for ffTK dihedral parameter optimization?

Hi Ernest,

The VMD parameterization tutorial has some good guidance (http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield.pdf, see the table on page 19). However, I kinda recognize these parameters. They SHOULD just be from the carbohydrate forcefield. For maximum transferability, I’d try to perturb the parameters for the pieces that are the same between mannose and your pyruvated mannose as little as possible (so the charges would be the same and the dihedrals would be too).

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Dec 21, 2016, at 2:02 AM, Ern Ong <Ern.Ong_at_student.adfa.edu.au<mailto:Ern.Ong_at_student.adfa.edu.au>> wrote:

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.