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#37546 - 06/30/19 08:58 AM THREE MEMBER RING warning
Nadia Offline
Forum Member

Registered: 05/11/07
Posts: 44
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?


Edited by Nadia (06/30/19 09:00 AM)

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#37547 - 06/30/19 11:33 AM Re: THREE MEMBER RING warning [Re: Nadia]
lennart Online   content

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Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
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.


Edited by lennart (06/30/19 11:34 AM)
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37549 - 07/01/19 05:29 AM Re: THREE MEMBER RING warning [Re: Nadia]
Nadia Offline
Forum Member

Registered: 05/11/07
Posts: 44
Perfect, thank you very much!

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