Dear .,
I am getting an unexpected error when I try to generate dihedral parameters
for a small molecule (I use Amber 18). To calculate the energies at
different dihedral values, I have tried to set restraints, but when I
minimize the molecule, it always comes out to be planar. I have tried many
combinations in the parameter files, as well as GAFF generated parameters -
but face the same issue.
The Folder:
https://1drv.ms/u/s!AnshjSOja1L6oVgwZVOQtPMYEch6?e=ShHdlS
has parameters I have derived (dihedrals are not completely fit yet).
I also tried a small MD with the above, just to check -- and the dihedral
is still planar. Results of the small MD are:
https://1drv.ms/u/s!AnshjSOja1L6oVe9G4zgJo6ULjWW?e=T0lTSb
I appreciate any insights you may have.
Best wishes, Prashanth
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Received on Sun Jun 23 2019 - 18:30:02 PDT
