Dear Ross,
Thank you for your suggestion.
On Mon, Apr 18, 2011 at 9:51 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Setyanto,
>
> > I choose atom number from the PDB file that create by leap.
> > When I made file preparation file using tleap usually I also save box
> > file
> > using SavePDB.
> >
> > Am I correct to choose atom numbers from PDB file that I got from tleap
> > ?
>
> I believe this is fine since I think xleap writes out pdbs with its
> internal
> numbering rather than the numbering in the original pdb. To double check
> though you should set write_pdb=1 in the qmmm namelist. Then when you run
> your QMMM calculation you will get a pdb of the QM region, including link
> atoms, which you can then visualize to make sure you got what you expected.
>
> Good luck,
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Tue Apr 19 2011 - 06:30:08 PDT
