[gmx-users] Ring planarity

[Mohsen Ramezanpour]

Dear Gromacs users,

I am working on a Protein-drug interaction problem.

The small molecule has a cytosine ring.

Based on QM calculations and PDB database, The structure for this ring
should be planar. However, doing simulations the the ring is not completely
planar . Besides, the NH2 group on it will make an angle with the ring
overall plane.

I was wondering if I should 1) halt the 1-4 interactions among the ring
atoms with neighbour atoms out of ring, 2) apply more strong improper
dihedrals force constants, or 3) this kind of deviations (from optimized
geometry in gas phase) is Ok. The latter case (#3) can be justified because
in the presence of protein and water, the overall energy of system might be
more favourable in this deformed structure, although a high energy might be
needed to deform a ring.

The same for NH2 group connected to the ring. Should I force it to stay in
the plane or let it go as it prefers?

Thanks in advance for your reply and comments
Cheers
Mohsen





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