It looks to me like one issue you likely have is that your cx-cx-n8 angle
in your frcmod file is 59.59 degrees. That small angle (with a huge force
constant) is probably one factor that is pulling that N up into a strange
angle.
Also, you should verify that you have two cx and one cu atom in your ring.
I also am no gaff expert, but I do not know what the n8 atom type is
supposed to be. I would have thought that nh would be appropriate for your
situation. Having said that, I see that there is a cx-cx-nh angle defined
in gaff.dat and its angle is 59.17 degrees. So maybe the angle in your
frcmod file is OK -- but that seems like a chemically-strange angle to me.
Regardless, I would suggest changing the atom type of your nitrogen to nh.
It is possible then that all of your parameters will be already defined
within gaff.dat and you will no longer need a frcmod file.
Maybe someone else who knows more about gaff can respond about why that
equilibrium angle is so small.
Good luck!
Brent
On Fri, May 26, 2017 at 6:37 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Very interesting now I see the pictures. I wonder if there's a
> possibility of torsions fighting with angles here.
>
> > which ones to specify
>
> It seems you have drawn them in? Not looking at your input files, it
> seems you might have Cx-Cy-N 118.0, and Hy-Cy-N 114.4 angles to define
> in your frcmod per the actual atom types and format rules.
>
> > how to get the correct values?
>
> 'Correct' may come down to 'adequate for a given purpose'. You can
> likely guess force constants and maybe better values from reading
> paper(s) on GAFF, but I've never done it myself.
>
> Bill
>
> On 5/26/17 3:19 AM, Loris Moretti wrote:
> > I guess the problem is the distortion of the tetrahedral symmetry of the
> carbon where the amine is attached to. Which of course is already distorted
> because such carbon is in a cyclopropyl, but with a simple minimization the
> problem gets clear. Here in attachment pictures of the initial coordinates
> and the minimized ones. The angles looks too distorted.
> >
> > So I thought I should add parameters for the angles. But how can I do it
> properly? which ones to specify and how to get the correct values? I guess
> I should leave some bending.
> >
> >
> > Thanks,
> >
> > Loris
> >
> >
> > ________________________________
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Sent: Friday, May 26, 2017 10:50:10 AM
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] add ligand parameters
> >
> > >From a chemistry-challenged reading, it sounds like you might not be
> > getting planarity where you expect it?
> >
> > If so, adding an improper torsion term may be the solution.
> >
> > Bill
> >
> >
> > On 5/26/17 1:45 AM, Loris Moretti wrote:
> >> Hi All,
> >>
> >>
> >> I have a ligand containing a cyclopropyl substituted with an amine
> group and I would like to simulate its dynamic behavior inside a protein.
> >>
> >> But the parameters I get from the usual procedure antechamber + parmck
> result in a distorted molecule. Here in attachment the minimal example as
> an initial molecule (ligand.mol2) with AM1-BCC charges, the ligand.frcmod
> produced by the command:
> >>
> >>
> >> parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod -s 2
> >>
> >>
> >> (from Ambertools17)
> >>
> >>
> >> I've also tried with parmchk (instead of parmchk2) and gaff (instead of
> gaff2) without improvement. The "leap" commands to produce the system and
> the parameters and the coordinates for the system (system_init.prm and
> system_init.crd). The md.in for the simulation settings and the
> trajectory system_md.cdf obtained with the command:
> >>
> >>
> >> sander -O -i md.in -o md.out -p system_init.prm -c system_init.crd -r
> system_md.rst -x system_md.cdf
> >>
> >>
> >> In the simulation is clear that the angle of the C-C-N (carbons of the
> cycle and the nitrogen) goes distorted and I understand I have to insert
> new parameters for such angle into the ligand.frcmod file. I guess I have
> to generate those values manually, how should I do that? I've tried to
> check but I couldn't find proper information about the procedure.
> >>
> >>
> >> Thanks in advance,
> >>
> >> Loris
> >>
> >>
> >>
> >> _______________________________________________
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> >
> >
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>
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--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Fri May 26 2017 - 04:30:02 PDT
