AMBER Archive (2009)

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

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Fri Nov 20 2009 - 09:25:30 CST

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.
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.

Thank you very much!

Best regards,
Andrew

20.11.09, 14:42, "FyD" <fyd_at_q4md-forcefieldtools.org>:

> Dear Andrew,
>
> At http://q4md-forcefieldtools.org/Help/Andrew/ZN2.off you will find,
> a FF library for ZN2+ with a total charge of +2 and "ZN" (not Zn) as
> atom type & atom name, ZN2 as residue/FF libary name - considering
> that Zn remains the chemical element.
>
> At http://q4md-forcefieldtools.org/Help/Andrew/tleap.cmd you will find
> a tleap script. I hope it will solve your problem when using:
> tleap -f tleap.cmd
>
> Pay attention at the _capital letter_ of Zinc when you consider the
> residue name, the atom name, the atom type or the chemical element.
>
> Does it help ?
>
> regards, Francois
>
>
> > Dear Francois, things still don\t work.
> >
> > I've saved Zn into a separate PDB file as in this tutorial:
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section2.htm
> >
> > Here are PDB file contents:
> > HETATM 1666 ZNA ZN A 1 -34.053 -24.945 -27.759 1.00 27.33 ZN
> > END
> >
> > Then I've loaded it as zna = loadpdb zna.pdb and tried to set the
> > atom type and charge according the command which yo have provided in
> > format set unit.resnumber.resname type Zn. But I've got an error
> > about that this is "not a containter".
> >
> >
> >> desc zna
> > UNIT name:
> > Head atom: null
> > Tail atom: null
> > Contents:
> > R
> >> set zna.1.ZN type Zn
> > zna.1.ZN: not a container (e.g. residue)
> > usage: set
> >> set zna.1.ZN charge 2
> > zna.1.ZN: not a container (e.g. residue)
> > usage: set
> >> set zna.1.Zn charge 2
> > zna.1.Zn: not a container (e.g. residue)
> > usage: set
> >>
> >
> >
> >
> > 18.11.09, 15:29, "FyD" :
> >
> >> Dear Andrew,
> >>
> >> > Your tutorials are about RESP chareges and I actually don t need
> >> > RESP charges here, only non Zn atom specification using tleap but
> >> > not GUI of xleap.
> >>
> >> I provided many links, Yes, with many different applications (may be
> >> too much, ok) - but, No, not only about RESP charges.
> >> For instance: the http://q4md-forcefieldtools.org/Tutorial/leap.php link
> >> provides examples of xLEaP commands in tLEaP.
> >>
> >> Concerning Zn, this is exactly as creating a new FF library for a
> >> new/non-standard residue. Either you decide to create a Zn2+ ion
> >> (similar to "MG2" for instance) with a total charge = +2, or you
> >> develop a new FF library for your Zn atom physically connected to the
> >> assumed ligands. In both cases, you will need a LEaP script (with
> >> charge values & FF atom types) as these I sent you.
> >>
> >> > I need the edit option in xleat, what is the analog in tleap where I
> >> > can Edit->Edit Selected Atoms
> >>
> >> If you follow the http://q4md-forcefieldtools.org/Tutorial/leap.php
> >> link (for instance - other links work as well):
> >> instead of using Edit->Edit xLEaP command, you can use the "set"
> >> command in tLEaP to define the type, charges, etc... See AMBER8 manual
> >> page 69:
> >>
> >> set ZN2 name "ZN2"
> >> set ZN2.1 name "ZN2"
> >> set ZN2 restype undefined
> >> set ZN2.1.Zn type Zn
> >> set ZN2.1.Zn charge 2
> >> etc...
> >>
> >> this is exaclty the same idea as
> >> http://q4md-forcefieldtools.org/REDDB/up/W-46/script1.ff
> >>
> >> After you check all with the "desc" command (AMBER8 manual, page 57):
> >> desc ZN2
> >> desc ZN2.1
> >>
> >> > desc MG2
> >> UNIT name: MG2
> >> Head atom: null
> >> Tail atom: null
> >> Contents:
> >> R
> >> > desc MG2.1
> >> RESIDUE name: MG2
> >> RESIDUE sequence number: 1
> >> RESIDUE PDB sequence number: 0
> >> Type: undefined
> >> Connection atoms:
> >> Improper torsions:
> >> Contents:
> >> A
> >> > desc MG2.1.MG
> >> ATOM
> >> Normal Perturbed
> >> Name: MG MG
> >> Type: MG MG
> >> Charge: 2.0000 0.000
> >> Polarization: 0.0000 0.000
> >> Element: Mg (not affected by pert)
> >> Atom flags: (decimal 131072 hex 0x20000)
> >> posfxd n posblt n posdrwn n selected n
> >> pert n notdisp n touched n posknwn Y
> >> internal n needsmin n needsbuild n
> >> Atom position: 0.000000, 0.000000, 0.000000
> >> Atom velocity: 0.000000, 0.000000, 0.000000
> >> NO BONDS
> >>
> >> I hope help this time ?
> >> Adding web links takes less time than providing explanations ;-)
> >>
> >> regards, Francois
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> > _______________________________________________
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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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