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Hello Olivier-- > I have been trying to create an isopeptide bond patch to join two > monomers of ubiquitin (Gly76->Lys48) using the amber force field > (needed for GB), but the result is that during minimization and > dynamics, I have the following output: > *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.001 > --* > | E(kin)+E(poten)= -66.620 E(kin)= 0.689 temperature= > 0.971 | > | E(poten)= -67.3086349 grad= 0.0000008 ANGL= > 0.0000000 | > | BOND= 0.0000000 IMPR= 0.0000000 VDW+GBIN+GBSE= > -67.3086349 | > *------------------------------------------------------------------------------* > It's difficult to imagine how the patch could zero out those enery terms. Do you get any errors or warnings? Does the same script without a patch statement also have the zero energies? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwiQWYACgkQPK2zrJwS/lbEZwCfTzag3MOcdtQxpAjsT9iWcPIT aCcAn0lJE76esOHFBJ0YDtxqzkRufgMs =/JrR -----END PGP SIGNATURE----- _______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
