I think you should feel free to contact the corresponding author of any
paper. They can't always help but it's probably the person with the most
information.
On Sun, Apr 26, 2020, 2:04 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
> 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
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> > > > > >
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Received on Sun Apr 26 2020 - 11:30:02 PDT
