Hello Armin,
In order to prepare a .prepin file you first need a proper 3D structure
(.pdb) of your ligand. Then you should derive partial charges (RESP)
charges for the atoms of your pdb.
These charges can be derived by using Gaussian09 or RESP server or simply
you can assign partial charges by using antechamber.
You can google about Gaussian or RESP server (RED server).
In antechamber,
you can assign the partial charges by MOPAC or sqm .
## antechamber -i abc.pdb -fi pdb -o abc.mol2 -fo mol2 -c bcc -s 2
the output of this (a .mol2 file) will be carrying information about the
assigned charges.
You need to submit this file for generation of the prepin file for using in
xLeap.
## antechamber -i abc.mol2 -fi mol2 -o abc.prepin -fo prepi -c bcc -at
gaff (or amber)
This will generate abc.prepin file for your molecule. This will contain the
atom name, type and coordinate information.
Next step is to derive the parameters for your molecule.
## parmchk -i abc.prepin -f prepi -o abc.frcmod
This will give the parameters required to load your molecule in xLeap.
Additionally, you should go through the antechamber tutorials at
http://ambermd.org/tutorials/basic/tutorial4b/
All the best!!!!
Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Thu, Jul 13, 2017 at 5:10 PM, ARMIN HODAEI <ahodaei15.ku.edu.tr> wrote:
> Dear AMBER users,
>
>
> Do you know how can I define CMP ligands in xLEAP? I know that
> the procedure is to create a prepin file in ANTECHAMBER, but I have no idea
> where to start. Has anyone done this before?
>
>
> Sincerely,
> --
> Armin Hodaei
> Department of Physics,
> Faculty of Arts and Sciences
> Koc University, Istanbul
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Received on Thu Jul 13 2017 - 05:30:05 PDT
