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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-----
