AMBER Archive (2004)

Subject: Re: AMBER: hbond analysis in ptraj(%occupied>1)

From: Thomas E. Cheatham, III (
Date: Thu Mar 25 2004 - 12:26:50 CST

> I used ptraj to do the hbond analysis. I got %occupied >1. Does
> that mean :971_at_O4 forms hbond with more than one water molecule or some
> else? By the way, could anyone please tell me what is the "lifetime" in
> the output?
  DONOR ACCEPTOR %occupied distance angle lifetime maxocc
| 15540 :971_at_O4 | solvent acceptor | 101.98 2.852 (0.14) 26.75 (14.75) 3.5 ( 5.7) 39


The hbond command bins all the interactions satisfying the criteria. In
the case of a solvent acceptor definition, this could involve more than a
single solvent. An occupancy > 100% suggests that there are more than a
single solvent molecule interacting with :971_at_O4 over the simulation. An
occupancy of 100% could mean that 1/2 of the time no solvent is
interacting and 1/2 of the time 2 waters are interacting or could mean a
single solvent is interacting all of the time. To break it down to a
specific water you would have to specify water explicitly as an acceptor.
This however will overload you with information since the lifetime for
bound water is short and therefore you would see lots of short term
interactions with indidividual waters (which is why we implemented the
generic "solventacceptor").

The maxocc is the maximum number of consecutive frames that the
interaction is found in the trajectory (i.e. 39 consecutive frames).

The lifetime is the average time an interaction occurred...

For example, assume that each space below represents 1ps and a star
means it is occupied:

         10 20 30 40 50
     ***** ***** ********** *****|

The occupancy would be 5 + 5 + 10 + 5 / 50 or 50%
The maxocc would be 10
The lifetime would be 5 + 5 + 10 + 5 / 4 = 6.25 ps (assuming 1 ps between
frames; the time per frame can be specified on the hbond command line)

Let me know if you need further clarification. Note that the newer
versions of ptraj dump out a little ascii schematic drawing of the time
course of the interaction.

(Also note that the hbond command is fairly general; if you wanted to
track ion interactions, for example, Na+, you could set solventdonor Na+
Na+, solventacceptor Na+ Na+ Na+; also if you want to have more than 6
possible interactions of "solvent" with a given site, you can increase
solventneighbor; if more than 6 interactions are detected at a single
time, the code will complain)


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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