-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi Rob--
>
> We are trying to dock two proteins using PRE data (sbmf mode). In the
> calculation we are using three mtsl conformers
> to represent each probe. The docking protocol works, but the the
> calculated VDW energies are quite large. The structures look ok (no
> protein overlap)
> so I think the high energies are because the
> analyze() function used in writeStructure() uses all of the atoms to
> calculate the VDW energy. As a result atomic overlap between the
> probe conformers are counted (presumably because they aren't sensitive
> to the constrain statement).
> I also get high VDW energies when I use XplorPot("VDW").calcEnergy() to
> calculate the VDW energy
>
> How can I calculate the VDW energies for atoms in the proteins in the
> complex and not the overlapped mtsl conformers?
>
I guess you are talking about the VDW energies printed in the output
structure file? If so how do they compare with the value from the final
minimization step in the log file(s)? They *should* be the same. If
they're large, perhaps it's due to overlap elsewhere in the structure?
You might upload your script and an output pdb to our secure upload
area accessed via:
http://nmr.cit.nih.gov/xplor-nih/download.cgi
[click on the upload file button after logging in.]
thanks--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/>
iEYEARECAAYFAkubpcoACgkQPK2zrJwS/lZm2gCfV5hF1LffGtU70MXlI9T9PHNL
0r0AmwXaAyLTBK95Oc4nWn4gW0KruJsd
=IU2P
-----END PGP SIGNATURE-----
