> can somebody tell me how the SHAKE algorithm in sander determines which
> atoms actually are hydrogens?
The bonds are grouped in the prmtop according to whether an H is
involved (i.e. 2 groups).
> Does the assignment of the element "H" to a new atom type in Leap with
>
> addAtomTypes {{"X" "H" "sp3"}}
>
> mean that SHAKE will treat the new type as hydrogen?
Here is the code in unitio.h for selecting bonds w/ H:
if (iAtomElement(aA) == HYDROGEN || iAtomElement(aD) == HYDROGEN) {
Since the 'Element' is referred to, I expect assigning the element
of "H" with addAtomTypes should do the trick.
Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Apr 06 2004 - 21:53:00 PDT
