THREE MEMBER RING warning

Posted by: Nadia

THREE MEMBER RING warning - 06/30/19 08:58 AM

Dear all,
I am designing a patch for an enzyme with a Cys residue coordinated to two Ni atoms. The geometry is such that a 3-member ring forms between the two Nickel atoms and the sulfur atom of the Cys. When I try to patch my protein to the active site metal atoms, CHARMM complains with
"***** LEVEL 0 WARNING FROM *****
***** THREE MEMBER RING FOUND, NO DIHEDRAL ADDED"
******************************************
Is there any way to circumvent this problem?
Posted by: lennart

Re: THREE MEMBER RING warning - 06/30/19 11:33 AM

It is just a warning, telling you that the automatic generation of dihedrals (based on the connectivity (the BONDs)) has not been performed for the three-membered ring. If this is OK for you, you don't have to do anything. If, for some reason, you want dihedral terms for the ring you can add them in the PRES.
Posted by: Nadia

Re: THREE MEMBER RING warning - 07/01/19 05:29 AM

Perfect, thank you very much!