Quoting Andrew Voronkov <drugdesign.yandex.ru>:
> This is kind of zinc finger and it is connected to four amino acids,
> not small molecule ligands. So in case of amino acids I should also
> define frcmod for this zinc atom and four amino acids which are
> bound to it? To construct frcmod file by antechamber or use the
> frcmod file which I've mentioned above?
> And the library in this case (saveoff zinc.lib) should also be
> defined for the zinc atoms and four amino acids to which it is
> connected, right?
If you want to consider the whole complex i.e. Zinc-connected to
amino-acids, you canNOT use what is available .
http://q4md-forcefieldtools.org/Help/Andrew/
You need to create a frcmod file + an off FF library for your Zn-amino
acid complex.
I do think Antechamber handles metal atoms.
regards, Francois
> 23.11.09, 17:06, "FyD" <fyd.q4md-forcefieldtools.org>:
>
>> 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 1311>.A
>> 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.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > Added missing heavy atom: .R.A
>> > 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.A and .R.A
>> > WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
>> >
>> > -- ignoring the warnings.
>> >
>> > Building topology.
>> > Building atom parameters.
>> > For atom: .R.A 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" :
>> >
>> >> 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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Received on Mon Nov 23 2009 - 09:30:03 PST
