Dear Amber users,
I simulate periodic molecular graphene oxide. I followed the tutorial at
https://ambermd.org/tutorials/advanced/tutorial1_orig/, where the method
for creating a topology for non-standard residues is discussed.
I create .pdb files of my periodic molecules and prepare .lib files for
every residue that I create from the GAFF force field.
My question is, is it possible to automatically build a topology using
tleap, where bonds, angles, dihedrals, and improper potential functions are
written across periodic conditions?
I found a tutorial
https://ambermd.org/tutorials/advanced/tutorial13/Topology.php where the
command "bond" is used to write a bond across the periodic image, but in
this case, I should also manually write angles, dihedrals, and impropers?
Is it possible to include in the .pdb file of my molecule information on
periodic box size to automatically generate periodic topology? Perhaps
another approach exists for writing bonded interactions across periodic
boundary conditions?
Best wishes,
Victor
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Received on Tue Dec 12 2023 - 02:00:03 PST
