Hi George,
In this case, you just have to check that the parameters found by parmchk
are "reasonable". $AMBERHOME/dat/leap/parm/gaff.dat has comments next to
each atom type that describes what atom type it's supposed to be. What
parmchk did was determine that there were atom types "similar" to the ones
in your ligand that had parameters associated with them, so it just used
those. If the choices were good ones, just load the frcmod and run with it.
There are times when parmchk can't find what it considers reasonable
parameters. In that case, it just gives 0.000 as every parameter and says
ATTN next to it. That's when you *know* you need to modify it.
Hope this helps,
Jason
On Sat, Apr 9, 2011 at 1:32 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Dan,
>
> I did run parmchk on the ligand.
>
> Here's the parmchk output
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
> cy-c2-c3 62.700 116.520 same as c3-c2-c3
> c2-cy-hc 47.030 110.490 same as c2-c3-hc
>
> DIHE
> cy-cy-c3-c3 1 0.156 0.000 3.000 same as X
> -c3-c3-X
> cy-cy-c3-hc 1 0.156 0.000 3.000 same as X
> -c3-c3-X
> cy-cy-c2-c3 1 0.000 0.000 2.000 same as X
> -c2-c3-X
> cy-cy-c2-c2 1 0.000 0.000 2.000 same as X
> -c2-c3-X
> c3-cy-c3-hc 1 0.160 0.000 3.000 same as
> hc-c3-c3-c3
> c3-c3-cy-hc 1 0.160 0.000 3.000 same as
> hc-c3-c3-c3
> c3-c2-cy-hc 1 0.000 0.000 2.000 same as X
> -c2-c3-X
> c2-c2-cy-hc 1 0.380 180.000 -3.000 same as
> hc-c3-c2-c2
> c2-c2-cy-hc 1 1.150 0.000 1.000 same as
> hc-c3-c2-c2
> hc-cy-c3-hc 1 0.150 0.000 3.000 same as
> hc-c3-c3-hc
>
> IMPROPER
> c2-c3-c2-cy 1.1 180.0 2.0 Using default
> value
> c2-ha-c2-ha 1.1 180.0 2.0 Using default
> value
>
> The angle parameters that are declared as missing by "check ligand" are
> shown in the frcmod file. I'm a bit lost on how to manually edit this one.
>
> Thanks again
>
> George
>
>
> On Apr 8, 2011, at 11:19 PM, Daniel Roe wrote:
>
> > Hi,
> >
> > Try running parmchk on your ligand, e.g.
> >
> > parmchk -i caryo.mol2 -fi mol2 -o caryo.frcmod
> >
> > This will generate a frcmod file with the missing parameters. You
> > should visually inspect these parameters to make sure they look
> > reasonable. See sections "4.1.2 parmchk" and "4.2 A simple example for
> > antechamber" in the AmberTools user manual for further examples.
> >
> > -Dan
> >
> > On Fri, Apr 8, 2011 at 5:07 PM, George Tzotzos <gtzotzos.me.com> wrote:
> >> Hi everybody,
> >>
> >> I'm trying to generate ligand input files for an MD ligand/protein
> simulation.
> >>
> >> My ligand is caryophyllene (see snapshot)
> >>
> >> The ligand caryo.pdb has been generated with Chimera and the caryo.mol2
> file with antechamber.
> >>
> >> Checking the unit ("check CARYO) gives the following output
> >>
> >>
> >> Checking 'CARYO'....
> >> Checking parameters for unit 'CARYO'.
> >> Checking for bond parameters.
> >> Checking for angle parameters.
> >> Could not find angle parameter: cy - c2 - c3
> >> Could not find angle parameter: c2 - cy - hc
> >> There are missing parameters.
> >> Unit is OK.
> >>
> >> I'm reluctant to continue given that the above parameters are missing.
> >>
> >> I'd appreciate any suggestion on solving this problem
> >>
> >> A good evening to all
> >>
> >> George
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 09 2011 - 10:30:03 PDT
