I am using ZAFF (
https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.php) to build an MM model of a Zn-coordinating protein where one of the coordinating centers is the oxygen of a water molecule. The ZAFF.prep file defines a new type of three-point water residue for this purpose. No trouble there.
The problem I’m running into is that because, just like e.g., TIP3P, this water molecule includes a bond between its two hydrogen atoms, pmemd complains that there are too many bonds to the hydrogen atoms:
“2014: 4076 - 4077 and 2016: 4075 - 4077
Hydrogen atom 4077 appears to have multiple bonds to atoms 4076 and 4077 which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.”
(Incidentally, I think there’s an off-by-one error in generating this error message – the second line says 4077 is bound to 4076 and 4077, but probably should say it’s bound to 4075 and 4076, as in the first line).
I’m pretty sure the “right” thing to do here is to somehow tell Amber to include this special water molecule in its definition of what SHAKE considers to be water molecules. I have tried providing more than one residue name to the WATNAM command in the &cntrl namelist, but no luck. How can I get SHAKE to consider two different residue names to be water? Or is there a workaround I should consider instead (other than just using a default water molecule instead of the special water)?
Thanks!
-Tucker
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 10 2024 - 08:30:03 PDT
