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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Received on Sun Apr 26 2020 - 09:00:02 PDT
