Sir,
Would it be okay to contact them directly through mail with the query?
On 26 Apr 2020 22:54, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> the Amber email help list is mostly questions about the software and how to
> use it. For problems or questions about the force fields it might also be
> good to contact the authors of the force field you are using, since that is
> often a different group that the people that usually answer things here.
> Sometimes people on the software list can answer force field questions, but
> sometimes not...
>
>
> On Sun, Apr 26, 2020 at 12:34 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
>
> > Sir,
> > I have checked the atom types and they seemed fine. So I got all more
> > confused. In the mailing list, there were previous queries of the same
> kind
> > in the past, but could not see an exact response or noone shared how they
> > dealt with it.
> > On 26 Apr 2020 21:20, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> > wrote:
> >
> > > 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 - 11:30:02 PDT
