AMBER Archive (2005)

Subject: Re: AMBER: ptraj Hbond analysis

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Wed Nov 16 2005 - 23:28:42 CST

> I have used ptraj to do some hbond analysis of an MD trajectory.
> I have some doubts about the results. The %occupied is greater than
> 1000 in many cases of solvent acceptor and solvent donor when the imaged
> trajectory is used.
> When the original trajectory is used the %occupied is around 700 in
> many cases.
> From the mail archive I understand that it means about 10 / 7 water
> molecules are hydrogen bonded to the particular atom.
> Is it normal?
> Which one is the correct method? The output obtained is attached.

At present the hbond facility does not image the distances, so it makes
sense that after imaging the occupancies are higher. (since waters that
were in adjacent periodic cells get imaged back). I will fix hbond to do
imaging in the future.

The next question is whether occupancies of > 100% up to 700-1000% are
reasonable. If ptraj is working correctly, this would mean that there are
between 7-10 waters interacting with the group (subject to no angle but a
3.5 A distance criteria). This seems high.

To verify, you could try calculating a radial distribution function around
the given groups to see if this many waters are within range.

You could be including waters within the second water shell using a 3.5 A
criteria (rather than say 3.2 A).

Since your hbond command uses the default parameter for solventneighbors
(i.e. 6) I find it problematic that 7-10 waters are found since a max of 6
would be tracked. Therefore this looks like a bug.

did you redefine solvent? This appears to be an old version of ptraj
since the maxocc column was not specified.

What version of ptraj are you using?

I'd be happy to help you try to track this down...

-- tec3_at_utah.edu

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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