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<MG2 1>
> desc MG2.1
RESIDUE name: MG2
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 0
Type: undefined
Connection atoms:
Improper torsions:
Contents:
A<MG 1>
> 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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Received on Wed Nov 18 2009 - 07:00:02 PST
