AMBER Archive (2004)

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

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Thu Mar 25 2004 - 12:54:59 CST

Thanks a lot. I really appreciate it.

Best,
Lishan

On Thu, 2004-03-25 at 13:26, Thomas E. Cheatham, III wrote:
> > 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
>
> Yes.
>
> 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)
>
> --tom
>
>
> \ 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
> |
> | tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> \ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham
>
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