Re: [AMBER] generate topology file and parameter file for complex with dummy atoms

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Sat, 29 Nov 2014 16:08:00 -0800

Dear Jason,

Thanks for the reply after that I was able to generate the parmeter and
library file. I can generate the parameter and starting coordinates fine.
As I am added dummy atoms to the complex they cannot be present in the
initial starting pdb so I did expect that tleap would generate the missing
coordinates - I have 6 dummy atoms but it crashes with the following error


ERROR: Comparing atoms
        .R<ZNA 363>.A<DD5 5>,
        .R<ZNA 363>.A<DD4 4>,
        .R<ZNA 363>.A<DD3 3>, and
        .R<ZNA 363>.A<DD2 2>
       to atoms
        .R<ZNA 363>.A<DD5 5>,
        .R<ZNA 363>.A<DD4 4>,
        .R<ZNA 363>.A<DD6 6>, and
        .R<ZNA 363>.A<DD2 2>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named DD6 from ZNA did not match !
!
!ABORTING.

I have tried to add TER to the file but no success only when all the atoms
are present it is fine. Have I missed something in the library file ?

Thanks






On Fri, Nov 28, 2014 at 3:53 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Fri, Nov 28, 2014 at 6:45 PM, Jorgen Simonsen <jorgen589.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am trying to generate an octahedral complex with dummy atoms to mimic
> > partial charges around the complex. As the complex is symmetric I have
> only
> > added three atom types DD1-3.
> >
>
> ‚ÄčI don't think atom types can have more than 2 letters in tleap, so I don't
> think this will work. Try cutting them down to 2 letters (and still use
> the frcmod file). One note, the dihedral section of the frcmod file should
> be of the format:
>
> XX-XX-XX-XX
>
> where each field is 2 characters (one space if it's a 1-letter atom type).
> In the snippet below, it looks like you have spaces in there.
>
> HTH,
> Jason
>
> The problem is that I am not able to save the parameter or the topology
> > file as tleap will not make them due to missing parameters:
> >
> > The first warning is this:
> >
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-DD6-DD7-*
> > +--- With Sp0 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-DD5-DD6-*
> > +--- With Sp0 - Sp0
> >
> >
> > I have not added a new atom type - maybe I should add one?
> >
> > The warnings continue with the following error message:
> >
> >
> > Building proper torsion parameters.
> > 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> >
> > 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> >
> > 1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> >
> > 1-4: angle 5 6 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> >
> > 1-4: angle 5 7 duplicates bond ('triangular' bond) or angle ('square'
> bond)
> >
> > and continues to give this warning/error
> >
> > ** No torsion terms for DZ3-ZN-DZ2-DZ4
> > ** No torsion terms for DZ3-ZN-DZ3-DZ4
> > ** No torsion terms for DZ3-ZN-DZ2-DZ4
> > ** No torsion terms for DZ3-DZ2-ZN-DZ4
> > ** No torsion terms for DZ3-DZ2-DZ3-DZ4
> > ** No torsion terms for DZ3-DZ4-ZN-DZ4
> > ** No torsion terms for DZ3-DZ4-DZ2-DZ4
> > ** No torsion terms for DZ3-DZ4-DZ3-DZ4
> > ** No torsion terms for DZ3-DZ4-DZ2-DZ4
> > ** No torsion terms for DZ3-DZ2-ZN-DZ4
> > ** No torsion terms for DZ3-DZ2-DZ3-DZ4
> > ** No torsion terms for DZ2-ZN-DZ2-DZ3
> > ** No torsion terms for DZ2-ZN-DZ2-DZ4
> >
> > and ends with the following message
> >
> > Building improper torsion parameters.
> > total 0 improper torsions applied
> > Building H-Bond parameters.
> > Incorporating Non-Bonded adjustments.
> > Parameter file was not saved.
> >
> > I have tried to add these to the frcmod-file
> >
> > DIHE
> > X -DZ2 -DZ3 -DZ4 1 0.0 35.3 2.00
> > X -ZN -DZ3 -DZ4 1 0.0 35.3 2.00
> >
> > IMPROPER
> > X -ZN -DZ -X 0.0 180. 2.
> > X -ZN -DZ -X 0.0 180. 2.
> > X -ZN -DZ -X 0.0 180. 2.
> > X -DZ -DZ -X 0.0 180. 2.
> >
> > but same amount of error mesages. I am using ambertools14 with the ff14SB
> > force field - any recommendation how to fix this would be highly
> > appreciated. Thanks
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Nov 29 2014 - 16:30:02 PST
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