Re: AMBER: problem with ptraj and randomizeions

From: Thomas E. Cheatham, III <>
Date: Thu, 17 Feb 2005 11:57:23 -0700 (Mountain Standard Time)

> I have a problem with the randomizeions command in ptraj. I would like

It is nice to see that someone is using this option to remove the initial
bias of targeted ion placement; however a bit worrisome that it is not
working fully correctly :-)

> randomizeions :Cl- around :1-436 by 5.0 overlap 3.5
> randomizeions :K+ around :1-436 by 5.0 overlap 3.5

Is it a Cl- ion? The parser may be mistakingly treating the minus as a
continuation character (try :Cl? instead).

Which ion is not being moved (i.e. the first or the last meaning perhaps
there is a +/- 1 error in the parser?).

If you start up rdparm, there is the "checkmask" command which will print
out what it thinks it has selected; you can check to see if this matches
all the ions you want to select...

   checkmask :Cl-

Which version of ptraj?

Good luck,

\ 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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Received on Thu Feb 17 2005 - 19:53:00 PST
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