AMBER Archive (2004)

Subject: Re: AMBER: which atoms are H's for SHAKE?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Apr 06 2004 - 15:11:41 CDT

> 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
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