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 Mon Apr 18 2011 - 08:00:03 PDT
