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Hello Valerie-- > > I noticed that I have very high energies for my two docked proteins (using > PRE as a restraint). I realized later that >99% of the high energies > are from the crystal structure input. I determined the solution > structure of the other protein, so I know what its energies are. Thus, > I had been using these input structures (one with very high energies) > for the docking script. > Unless you have additional experimental data for the crystal structure, perhaps it's best just to leave it as is. You can add protons using regularize.addUnknownAtoms, or the XPLOR hbuild statement. If the high energies bother you, you can use a constraints interaction statement to exclude them. If you were to try to fix-up the crystal structure- optimally, you could include the Xray data... best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkp8NlEACgkQPK2zrJwS/lZ5gwCdFncAABfBxnsPcmYezlQLGBY0 j50AnjksGoDQpZ2mIKv0TylwpsNLB41a =TyYm -----END PGP SIGNATURE-----
