AMBER Archive (2007)

Subject: Re: AMBER: energy minimization parameter

From: Lorenzo Gontrani (l.gontrani_at_caspur.it)
Date: Wed Aug 29 2007 - 02:54:58 CDT

Alle 09:54, mercoledì 29 agosto 2007, Qiang Zhong ha scritto:
> Dear Amber users:
> I am study the TUTORIAL A8: Loop dynamics of the HIV-1
> integrase core domain.
> I cann't understand some content of min.in.the file content is below:
> Minimization with Cartesian restraints for the solute
> &cntrl
> imin=1, maxcyc=200,
> ntpr=5,
> ntr=1,
> &end
> Group input for restrained atoms ///what meaning of this line, it
> is just comment?
You are right, it is just a comment (or title)
> 100.0
> ///what meaning of this line, it is box size?
No, it is the amplitude of force constant (100.0 Kcal/mole)
> RES 1 155
> END
> END
>
> I don't know what meaning of comment line,Could somebody tell me what
> meaning it is?
>
>
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Hope this helps (and I am right!)

Lorenzo 

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Lorenzo Gontrani

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