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Tinker: Software Tools for Molecular Design
https://dasher.wustl.edu/tinker/
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OPLSAA-M torsional parameters in oplsaam.prm file. #149

Closed BernardUPSaclay closed 3 months ago

BernardUPSaclay commented 6 months ago

I would like to use torsion parameters for the peptide backbone to model PBLG (poly gamma-benzyl L-glutamate). I compare data in the Robertson-2015-JCTC paper and the oplsaa.prm, oplsaal.prm and oplsaam.prm files of tinker 8.10.5 distribution. Although oplsaa and oplsaal parameters correspond to those in Robertson paper, I find that parameters given in oplsaam.prm are different from those given in Robertson-2015 but are identical to those in oplsaal.prm.

E.g. the angle phi (C-N-Calpha-C) along the peptide backbone is described by the following atom CLASS (classes are different for oplsaa and oplsaa-l/m) :

file        CLASS          V1/V2/V3                    V1/V2/V3
                          Robertson                   .prm files
-------------------------------------------------------------------------------
oplsaa    3-24-13-3    -2.365 / 0.912 / -0.85       -2.365 / 0.912 / -0.85
oplsaal  21-23-1-21    -0.596 / 0.279 / -4.913      -0.596 / 0.279 / -4.913
oplsaam  21-23-1-21    -2.511 / 0.21  / -0.200      -0.596 / 0.279 / -4.913

I find the same behavior for other angles along the peptide backbone.

Did I do some stupid mistake or misunderstood something in Robertson paper or tinker files organization? Or is there something wrong in the files?

jayponder commented 3 months ago

The OPLSAA-M parameters are something we were/are working on adding to Tinker. That file was never intended to be included in the GitHub release, as it was incomplete. It has been since been removed from the Tinker repo. Sorry for the confusion and inconvenience.