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Hello Irina-- > > I have built my small molecule with XPLOR, so now I have both psf and pdb > files. > > In general, to perform a simulated annealing for the complex of protein and > small molecule do I have to keep a small molecule rigid to get it in proper > orientation and without distorsion of its structure? this is a bit of a judgement call on your part. I'd definitely keep rigid those portions for which you know the geometry. If the molecule contains rotatable bonds, but you have a good idea of its configuration, fix the geometry. In any case, you might perform initial calculations with a rigid conformation. I hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFHh/KmPK2zrJwS/lYRAmrwAJ4qg3hYksjJpYi+vzF+IT+29nujnACfbwty gsgfwUiSuK6F2uuvEhdrYmk= =Rw6m -----END PGP SIGNATURE-----
