You need to create an frcmod file that has these terms in them. The problem
is that you've created a bond between a gaff atom type and an amber atom
type. Parameters do not exist. You can solve this in one of 2 ways.
First, you can re-define your ligand using amber atom types when you run
antechamber instead of gaff atom types (see the manual for how to do this,
it's just changing a single flag). The second is what I said above,
creating an frcmod file with these missing terms defined in them. You can
get these from either parm99.dat or gaff.dat, but you'll have to hunt around
for the right terms a little.
Good luck!
Jason
On Mon, Jul 19, 2010 at 5:45 PM, arikcohen <arikcohen.ucla.edu> wrote:
> Thanks again for all your great help!. I'm sorry for bothering you
> again but I have no choice in the matter.
> After creating the bond between the two atoms(C6 and Lys NZ), I'm
> getting the following error:
>
> leap.log:Could not find bond parameter for: N3 - c3
> leap.log:Could not find angle parameter: H - N3 - c3
> leap.log:Could not find angle parameter: H - N3 - c3
> leap.log:Could not find angle parameter: N3 - c3 - c3
> leap.log:Could not find angle parameter: N3 - c3 - oh
> leap.log:Could not find angle parameter: N3 - c3 - h1
> leap.log:Could not find angle parameter: N3 - c3 - c3
> leap.log:Could not find angle parameter: CT - N3 - c3
> leap.log:Could not find bond parameter for: N3 - c3
> leap.log:Could not find angle parameter: CT - N3 - c3
> leap.log:Could not find angle parameter: N3 - c3 - c3
> leap.log:Could not find angle parameter: N3 - c3 - oh
> leap.log:Could not find angle parameter: N3 - c3 - h1
> leap.log:Could not find angle parameter: N3 - c3 - c3
> leap.log:Could not find angle parameter: H - N3 - c3
> leap.log:Could not find angle parameter: H - N3 - c3
> leap.log: ** No torsion terms for CT-N3-c3-c3
> leap.log: ** No torsion terms for CT-N3-c3-oh
> leap.log: ** No torsion terms for CT-N3-c3-h1
> leap.log: ** No torsion terms for CT-N3-c3-c3
> leap.log: ** No torsion terms for H-N3-c3-c3
> leap.log: ** No torsion terms for H-N3-c3-oh
> leap.log: ** No torsion terms for H-N3-c3-h1
> leap.log: ** No torsion terms for H-N3-c3-c3
> leap.log: ** No torsion terms for H-N3-c3-c3
> leap.log: ** No torsion terms for H-N3-c3-oh
> leap.log: ** No torsion terms for H-N3-c3-h1
> leap.log: ** No torsion terms for H-N3-c3-c3
>
>
> I would be most thankful if you could instruct me as to the file that
> needs to be changed. Do I need to change it manually or from with in the
> tleap script? if manually, which file needs to be changed(.lib?) and in
> addition to what the N3 atom corresponds to as this is a converted name
> of amber(I guess), but to which atom ?. is this the new name for my
> catalytic lysine NZ atom ?
>
> Thanks again
>
> Arik
>
> On 7/19/2010 11:47 AM, arikcohen wrote:
> > Thanks a lot for your ultrafast response and above all your help.
> >
> > Arik
> >
> > On 7/19/2010 11:20 AM, Jason Swails wrote:
> >> Hello,
> >>
> >> I've put my comments below.
> >>
> >> On Mon, Jul 19, 2010 at 2:04 PM, arikcohen<arikcohen.ucla.edu> wrote:
> >>
> >>> Dear Members,
> >>>
> >>> I would be most thankful for any help in the following: I'm trying to
> >>> set up a covalent bond between my substrate and a catalytic lysine.
> >>>
> >>> The tleap script is the following: (the substrate was named as HPD)
> >>>
> >>> source /u/local/apps.old/amber8/serial/dat/leap/cmd/leaprc.gaff
> >>> source /u/local/apps/amber/10/dat/leap/cmd/leaprc.ff99SB
> >>>
> >> The paths are not needed. Also, why are you using leaprc.gaff from
> amber8
> >> and leaprc.ff99SB from amber10? Just change these two lines to:
> >>
> >> source leaprc.ff99SB
> >> source leaprc.gaff
> >>
> >> That should do it.
> >>
> >>
> >>> loadamberprep DERACognateSub.prepin
> >>>
> >>> loadamberparams DERACognateSub.frcmod
> >>>
> >>> enzyme_design = loadpdb DERA_MonCogSub_NoH.1.pdb
> >>>
> >> Your unit name is now enzyme_design
> >>
> >>
> >>> set enzyme_design head LYN.167.NZ
> >>>
> >>> set HPD tail HPD.252.C6
> >>>
> >> You do not need these. Furthermore, the the atom specification should
> be
> >> "unit.residue#.atom". Your unit is enzyme_design, not the name of the
> >> residue. In order to create a bond, just see the "bond" command in
> leap.
> >> It seems that what you want is:
> >>
> >> bond enzyme_design.167.NZ enzyme_design.252.C6
> >>
> >>
> >>> check enzyme_design
> >>>
> >>> charge enzyme_design
> >>> .
> >>> .
> >>> .
> >>>
> >>> The output which I'm getting is the following:
> >>>
> >>> >
> >>> > set enzyme_design head LYN.167.NZ
> >>> The value must be of the type: Atom
> >>>
> >> I explained this error above, but again, this command is not needed
> >>
> >>
> >>> >
> >>> > set HPD tail HPD.252.C6
> >>> The value must be of the type: Atom
> >>> >
> >>> > check enzyme_design
> >>> Checking 'enzyme_design'....
> >>> ERROR: The unperturbed charge of the unit: -4.805188 is not integral.
> >>> WARNING: The unperturbed charge of the unit: -4.805188 is not zero.
> >>>
> >> This is pretty self-explanatory. This is almost certainly due to your
> >> ligand having a non-integer charge. This is not close enough to an
> integer
> >> to be round-off error (or something similar), so I would double-check
> your
> >> charge derivation method for your ligand. If you need to redo it,
> consider
> >> R.E.D. tools. There is a link to it on the amber website.
> >>
> >>
> >> Hope this helps,
> >> Jason
> >>
> >>
> >>> I thank you in advance for your help
> >>>
> >>>
> >>> Arik
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 19 2010 - 19:00:03 PDT
