AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 23 2009 - 10:06:01 CST

Andrew,

You have two possibilities:

- either you consider your Zinc atom not connected to your ligand and
you only need vdW paramaters for this Zinc atom (consequently, the
total charge of your Zinc = +2)
In this case, you DO use the files available @
http://q4md-forcefieldtools.org/Help/Andrew/

- or you consider your Zinc atom connected to well-characterized
ligands and you will have to define bond, angle and dihedral FF
parameters as well (but the charge of the Zinc atom should not be = 2).
In this case, you canNOT use the files available @
http://q4md-forcefieldtools.org/Help/Andrew/
and you will have to define a FF library for "Zinc & its ligands" all
together.

Does it help ?

regards, Francois

> Where in this case I should get dihedrals and bond length, from my
> protein or this are some standarts?
>
> I've taken frcmod.zinc from this page:
> http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
>
> as far as in protein which I study zin is also tetrahedron
> coordinated then it should be ok. frcmod.zinc is below.
> The Zn parameters loads ok (I tried to replace Zn to Zn2 in
> frcmod.zinc, but no luck). I get the same for atom: .R<ZN2
> 1311>.A<ZN 1> Could not find type: ZN.
> Maybe this is still some PDB syntax problem or syntax with some
> atom-residues type in .off file against frcmod and(or) PDB?
>
>
> Amber Force Field Parameters for the Tetrahedron-Shaped Zinc Divalent Cation
> Loading library: ./ZN2.off
> Loading PDB file: ./2rf5-znparm.pdb
> Added missing heavy atom: .R<MET 1207>.A<CG 8>
> Added missing heavy atom: .R<MET 1207>.A<SD 11>
> Added missing heavy atom: .R<MET 1207>.A<CE 12>
> Added missing heavy atom: .R<PHE 1208>.A<CG 8>
> Added missing heavy atom: .R<PHE 1208>.A<CD1 9>
> Added missing heavy atom: .R<PHE 1208>.A<CD2 17>
> Added missing heavy atom: .R<PHE 1208>.A<CE1 11>
> Added missing heavy atom: .R<PHE 1208>.A<CE2 15>
> Added missing heavy atom: .R<PHE 1208>.A<CZ 13>
> Added missing heavy atom: .R<THR 1265>.A<CG2 7>
> Added missing heavy atom: .R<THR 1265>.A<OG1 11>
> Added missing heavy atom: .R<CGLU 1310>.A<OXT 16>
> total atoms in file: 1665
> Leap added 1628 missing atoms according to residue templates:
> 12 Heavy
> 1616 H / lone pairs
>> saveamberparm MOL tnk.prmtop tnk.inpcrd
> Checking Unit.
> WARNING: There is a bond of 4.409856 angstroms between:
> ------- .R<PRO 1282>.A<C 13> and .R<LEU 1283>.A<N 1>
> WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> For atom: .R<ZN2 1311>.A<ZN 1> Could not find type: ZN
> Parameter file was not saved.
>>
>
>
>
> The frcmod file is below:
>
>
> Amber Force Field Parameters for the Tetrahedron-Shaped Zinc Divalent Cation
> MASS
> DZ 3.0
> Zn 53.380
>
> BOND
> DZ-Zn 640.0 0.90
> DZ-DZ 640.0 1.47
>
> ANGLE
> DZ-Zn-DZ 55.0 109.50
> DZ-DZ-DZ 55.0 60.0
> DZ-DZ-Zn 55.0 35.25
>
> DIHE
> Zn-DZ-DZ-DZ 1 0.0 35.3 2.00
> DZ-Zn-DZ-DZ 1 0.0 120.0 2.00
> DZ-DZ-DZ-DZ 1 0.0 70.5 2.00
>
> IMPROPER
>
> NONB
> DZ 0.000 0.00
> Zn 3.100 1.0E-6
>
>
>
> 23.11.09, 14:25, "FyD" <fyd_at_q4md-forcefieldtools.org>:
>
>> Andrew,
>>
>> This frcmod file should only contains vdW parameters:
>> This takes 3 sec to do it by hands.
>> When you do all automatically, you do not understand what you do...
>> You just need to find these vdW parameters in the required paper:
>> See http://ambermd.org/Questions/mail/64.html
>>
>> See http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd
>> http://q4md-forcefieldtools.org/Help/Andrew/frcmod.zinc
>> replace xxxx yyyy by the Zinc vdW parameters...
>>
>> regards, Francois
>>
>>
>> > Hm, frcmod should be prepared by antechamber. Now we got antechamber
>> > error here:
>> >
>> > $ antechamber -i zn2.pdb -fi pdb -o zn2.prepin -fo prepi -c bcc -s 2
>> >
>> > Running: /amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>> > ANTECHAMBER_AC.AC -p gaff
>> >
>> > Total number of electrons: 0; net charge: 0
>> >
>> > Running: /amber10/bin/mopac.sh
>> > Error: unable to find mopac charges in mopac.out
>> >
>> > This is zn2.pdb, maybe there is something wrong with PDB file:
>> >
>> > HETATM 1666 ZN ZN2 1 -34.053 -24.945 -27.759 1.00 27.33
>> > ZN
>> > END
>> >
>> >
>> >
>> > 20.11.09, 18:47, "FyD" :
>> >
>> >> Quoting Andrew Voronkov :
>> >>
>> >> > Ok, interesting. The "Unknown residue" message doesn't appear
>> >> > anymore while loading pdb...but I have now problem in saving amber
>> >> > params files:
>> >> >
>> >> > Building topology.
>> >> > Building atom parameters.
>> >> > For atom: .R.A Could not find type: ZN
>> >> > Parameter file was not saved.
>> >>
>> >> See updated http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd
>> >> & BTW do not forget to prepare a "frcmod" file for setting vdW
>> >> parameters for your Zinc atom, I forgot to add this step
>> >>
>> >> F.
>> >>
>> >>
>> >> > 20.11.09, 16:40, "FyD" :
>> >> >
>> >> >> Andrew,
>> >> >>
>> >> >> > Yes! It works now! The problem was that I've changed the
>> atom name
>> >> >> > rather than residue name in PDB and also residue name was also
>> >> >> > shifted a bit left and was at last stage not ZN2 but N2.
>> >> >>
>> >> >> ok. This is a classical problem of recognition between
>> your PDB & the
>> >> >> FF libraries you load in LEaP.
>> >> >>
>> >> >> > I also wonder if it's ok to setup charge Zn2+ to a metal
>> ion bound
>> >> >> > to four amino acids or I should set up it as part of the
>> >> protein then.
>> >> >>
>> >> >> Two approaches are possible:
>> >> >> - The 1st one you consider Zn2+ not physically connected to your
>> >> >> ligands & the total charge of the atom Zn is +2 (BTW do
>> not forget to
>> >> >> prepare a "frcmod" file for setting vdW parameters for
>> your Zinc atom,
>> >> >> I forgot to add this step @
>> >> >> http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd).
>> >> >> - The second one you derive charges for your Zn-complex
>> were you will
>> >> >> consider connections between Zinc & well-established
>> ligands. In this
>> >> >> case, the charge of Zn2+ should decreased to... some value ;-)
>> >> >> I suggest you to use R.E.D.-III.3 and/or R.E.D. Server/R.E.D.-IV in
>> >> >> the latter case.
>> >> >>
>> >> >> regards, Francois
>>
>>
>>
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>>
>>
>
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>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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