As I remember I was trying to do something with zinc, I wonder if I need to do the same with magnesium.
As I remember I have made manually .frcmod file which I have then converted to prepin file, which I have used to create the zinc.off file library, which I have loaded
when I was parametrizing the protein.
I wonder if I need to do the same with the magnesium ion, or not. I also rememebr that I have used command set charge to set the charge to the zinc ion...that was I guss befor saving zinc.off file maybe....
> desc mg
UNIT name:
Head atom: null
Tail atom: null
Contents:
R<MG 300>
> set charge +2 300
set: Argument #2 is type Double must be of type: [string]
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set charge +2 MG 300
set: Improper number of arguments!
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
>
Best regards,
Andrew
[voronkov.t60-2 rab23]$ tleap
-I: Adding /home/osolodkin/amber10/dat/leap/prep to search path.
-I: Adding /home/osolodkin/amber10/dat/leap/lib to search path.
-I: Adding /home/osolodkin/amber10/dat/leap/parm to search path.
-I: Adding /home/osolodkin/amber10/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff
----- Source: /home/osolodkin/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /home/osolodkin/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/osolodkin/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> mg = loadpdb mg.pdb
Loading PDB file: ./mg.pdb
Unknown residue: MG number: 0 type: Terminal/last
.relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: MG sequence: 300
Created a new atom named: MG within residue: .R<MG 300>
total atoms in file: 1
The file contained 1 atoms not in residue templates
> set charge mg 2+
set: Argument #2 is type Unit must be of type: [string]
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set charge 2+ mg
set: Argument #2 is type Double must be of type: [string]
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
20.10.10, 17:36, "Dmitry Nilov" <nilovdm.gmail.com>:
> You should use both protein (for example ff99SB, describing protein
> and MG) and gaff (describing ligand) force fields simultaneously:
>
> tleap -s -f leaprc.ff99SB
> > source leaprc.gaff
> > loadamberparams ligand.frcmod
> > loadoff ligand.lib
> > mol = loadpdb protein.pdb
> > saveamberparm mol protein.prmtop protein.inpcrd
>
>
>
> On Tue, Oct 19, 2010 at 6:12 PM, Andrew Voronkov wrote:
> > Dear Amber users,
> > I have a biotarget which has magnesium ion together with the small molecule in the binding site. I have made parametrization in GAFF with antechamber for the ligand, but then I've gota šproblem with magnesium ion. I actually was sure that it is included in the Amber force fields as Na+ ions and I can't find much information in manuals about this. Should I include magnesium ion in the protein or in small ligand or make a separate library for it? Should I use gaff or protein force field?
> >
> >> saveamberparm rab 1z2ang_w.prmtop 1z2ang_w.inpcrd
> > Checking Unit.
> > FATAL: šAtom .R.A does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> >
> > Sincerely yours,
> > Andrew
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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Received on Wed Oct 20 2010 - 09:30:04 PDT
