There is no magic in MD and modeling.
The conformations you see come from your force field parameters and your
MD settings (how long you run, dt, pressure, etc)
In your case, the reason for the bending comes from the parameters.
Now, we do not know if that bending is reasonable or not, only you would
know, looking at the literature and knowing your system.
If you decide it should not bend, then you need to look at the force
field parameters you are using.
If you used gaff/antechamber to get those parameters, you should look
carefully and that step, at the frcmod file, etc and change parameters
there.
My suspicion is that the force constants for your torsions in the rings
are not strong enough, but I cannot really confirm that.
adrian
On 3/12/20 11:25 AM, Sruthi Sudhakar wrote:
> [External Email]
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_drive_folders_1zy084puRN-5FRDyFg2DWPfTXNG65QznHsh-3Fusp-3Dsharing&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=DuufnE42idtT6iqcpgOIVxFyZxSKuwKxbyKTH6V8GAk&s=PkWeRXi4TPQVifmicvd2VuRKDNTQDQCxJXJHt8jrvKw&e=
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> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=DuufnE42idtT6iqcpgOIVxFyZxSKuwKxbyKTH6V8GAk&s=7XIG5DFYHu3--aISC18C-II4Y9QvEVDMPIBiBLQyJ48&e=
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Mar 12 2020 - 09:00:02 PDT
