AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Nov 20 2009 - 07:42:58 CST

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<ZN 1>
>> set zna.1.ZN type Zn
> zna.1.ZN: not a container (e.g. residue)
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
>> set zna.1.ZN charge 2
> zna.1.ZN: not a container (e.g. residue)
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
>> set zna.1.Zn charge 2
> zna.1.Zn: not a container (e.g. residue)
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
>>
>
>
>
> 18.11.09, 15:29, "FyD" <fyd_at_q4md-forcefieldtools.org>:
>
>> 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
>>
>>
>>
>> _______________________________________________
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>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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>
>

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

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