Respected group members,
I have run simulation on a G -Quadruplex- ligand complex. Our ligand has
two aromatic fused rings, One of which is a quinolinium ring and the
nitrogen has a positive charge. The quinolinium ring remained planar till
the heating stage, but got slightly distorted from the density
equilibration stage onwards.
After production, I have done the clustering and observed the
representative frame of the major ensemble in pymol and could see a polar
contact within the system. Is this kind of distortion in the geometry of a
planar aromatic quinolinium like ring is normal? If not, I request you to
kindly suggest some way out.
Please find the attached snapshots of the cluster and the density
equilibrated structures below.
Respected group members,
I have run simulation on a G -Quadruplex- ligand complex. Our ligand has
two aromatic fused rings, One of which is a quinolinium ring and the
nitrogen has a positive charge. The quinolinium ring remained planar till
the heating stage, but got slightly distorted from the density
equilibration stage onwards.
After production, I have done the clustering and observed the
representative frame of the major ensemble in pymol and could see a polar
contact within the system. Is this kind of distortion in the geometry of a
planar aromatic quinolinium like ring is normal? If not, I request you to
kindly suggest some way out.
Please find the attached snapshots of the cluster and the density
equilibrated structures below.
Respected group members,
I have run simulation on a G -Quadruplex- ligand complex. Our ligand has
two aromatic fused rings, One of which is a quinolinium ring and the
nitrogen has a positive charge. The quinolinium ring remained planar till
the heating stage, but got slightly distorted from the density
equilibration stage onwards.
After production, I have done the clustering and observed the
representative frame of the major ensemble in pymol and could see a polar
contact within the system. Is this kind of distortion in the geometry of a
planar aromatic quinolinium like ring is normal? If not, I request you to
kindly suggest some way out.
Please find the attached snapshots of the cluster and the density
equilibrated structures below.
https://drive.google.com/drive/folders/1zy084puRN_RDyFg2DWPfTXNG65QznHsh?usp=sharing
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Received on Thu Mar 12 2020 - 08:30:01 PDT
