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 - 05:35:31 CST

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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber