Could you just tell me if the -nc flag is really necessary during the resp
fit if our ligand has a net charge?
On 26 Apr 2020 23:58, "Jenny 148" <jenny.rs140.gmail.com> wrote:
> Thank you sir. I would do that.
> On 26 Apr 2020 23:54, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
>
>> 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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>> > > > > > >
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Received on Sun Apr 26 2020 - 14:30:02 PDT
