I'm not a GAFF expert, so Junmei's input here would be great, but what I
would do would be to look at the atom type assignments, not just the
parameters in the frcmod. Are the atoms that are becoming non-planar
assigned atom types consistent with sp2 or sp3 geometries? Once the atom
types are assigned then you end up with parameters, but maybe it's a
chemical perception problem. I'd check that first.
On Sun, Apr 26, 2020 at 11:34 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:
> Respected all,
> Even I am facing the same issue using AMBER18 recently. The procedure I
> followed is almost similar, but my ligand is combined to a G-quadruplex
> structure in tleap. But in frcmod file, even I am getting such high penalty
> scores and my aromatic ligand also shows planarity distortion. Have
> enquired regarding the same sometime back but did not get any response.
> Hope this time someone might be able to give some insight on this.
> Thank you
>
> On Sun, Apr 26, 2020 at 10:20 AM Jenny 148 <jenny.rs140.gmail.com> wrote:
>
> > > Dear all,
> > >The following is a recurring problem and I have repeated the simulation
> > multiple times and still the issue persists. Please help.
> > I have done a simulation on an aromatic ligand which must remain planar.
> I
> > optimized the structure in Gaussian, done docking on the ligand,
> calculated
> > ESP charges for selected conformers in Gaussian again. My ligand has a +2
> > charge. Then I have done the RESP fitting using antechamber and generated
> > the frcmod file.(AMBER18)
> > > antechamber -fi gout -i ligand.log -fo prepi -o ligand.prepi -c resp
> > > parmchk2 -i ligand.prepi -o ligand.frcmod -f prepi.
> > >
> > > Then I performed restrained minimization, heating and density
> > equilibration and unrestrained equilibration and 500ns production. My
> > ligand strangely loses the planarity by the equilibration stage and
> shows a
> > really distorted structure which is unacceptable. I have used the gaff ff
> > and Tip3p waterbox in the simulation. My frcmod file looks like the
> > following:
> > > DIHE
> > > ca-ca-cc-cc 4 2.800 180.000 2.000 same as X
> > -c2-ca-X , penalty score=232.0
> > > ca-ca-cc-cf 4 2.800 180.000 2.000 same as X
> > -c2-ca-X , penalty score=232.0
> > > ca-cc-cf-ha 4 16.000 180.000 2.000 same as X
> > -cc-cd-X , penalty score=136.0
> > > ca-cc-cf-cf 4 16.000 180.000 2.000 same as X
> > -cc-cd-X , penalty score=136.0
> > > cc-cc-cf-ha 4 16.000 180.000 2.000 same as X
> > -cc-cd-X , penalty score=136.0
> > > cc-cc-cf-cf 4 16.000 180.000 2.000 same as X
> > -cc-cd-X , penalty score=136.0
> > >
> > > IMPROPER
> > > c3-ca-na-cc 1.1 180.0 2.0 Using the
> > default value
> > > ca-ca-ca-na 1.1 180.0 2.0 Using the
> > default value
> > > ca-ca-ca-cc 1.1 180.0 2.0 Using the
> > default value
> > > ca-ca-ca-ha 1.1 180.0 2.0 Using
> general
> > improper torsional angle X- X-ca-ha, penalty score= 6.0)
> > > cc-h4-cc-na 1.1 180.0 2.0 Using the
> > default value
> > > ca-cc-cc-cf 1.1 180.0 2.0 Using the
> > default value
> > > cc-cf-cf-ha 1.1 180.0 2.0 Same as X
> -X
> > -ca-ha, penalty score= 46.8 (use general term))
> > > c3-ca-na-cd 1.1 180.0 2.0 Using the
> > default value
> > > cc-h4-cd-na 1.1 180.0 2.0 Using the
> > default value
> > > cc-cd-cc-ha 1.1 180.0 2.0 Same as X
> -X
> > -ca-ha, penalty score= 38.9 (use general term))
> > > Could someone suggest what might have went wrong and how to solve this
> > issue. I am attaching the image of my distorted ligand here.
> > > My two major doubts are
> > > 1. Is the frcmod file wrong?
> > > 2. should I include the -nc flag in the resp fitting since my ligand
> has
> > a +2 charge?
> > When I repeated the procedure to an old ligand which we had then
> simulated
> > in AMBER14, the newly generated frcmod files have same components as the
> > old files,but with a high penalty score. Is there something peculiar we
> > should mention in the latest version?
> > > Thanks in advance
> > >
> > > --
> > > Jenny R.S
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Apr 26 2020 - 09:00:03 PDT
