[gmx-users] 15-20% tolerance?

[David]

On Wed, 2004-03-31 at 19:17, xiaobing tian wrote:
> Dear David and Dallas,
>  
> Is it OK to increase the tolerance to 15-25%?
I don't care... If you think there should be a SS bridge do whatever you
like to get it...

As a general rule 10% should be enough. There are also ions that are
coordinated by Cys residues, and we don't want to create chemical bonds
between these ligands.

>  
> Thanks,
>  
> Xiaobing
> 
> David <spoel at xray.bmc.uu.se> wrote:
>         On Wed, 2004-03-31 at 16:51, xiaobing tian wrote:
>         > Dear Dr. Warren,
>         > 
>         > Thank you for your explanation. By the way, besides
>         compiling it, are
>         > there any other solutions to edit the SS tolerance?
>         > 
>         
>         No.
>         
>         But you can still edit your coordinate file such that the
>         appropriate
>         sulphurs are within the limits. Use a text editor...
>         
>         > Have a good day,
>         > 
>         > Xiaobing
>         > Dallas Warren wrote:
>         > >Thank you for your kind reply. However, I didn't untar the
>         > Gramcs file. I 
>         > >just download the gromacs-3.2.1-i386.rpm to /root directory
>         > and installed 
>         > >it at same directory in my Linux Red Hat 8.0. In this case,
>         > where is it 
>         > >possibly?
>         > 
>         > I am sure the developing guys will answer when it comes
>         around
>         > to t heir day 
>         > time, but I suspect that it doesn't exist on that machine
>         > since the .c file 
>         > is a program/script file written in C and is compiled to
>         > produce the 
>         > appropriate GROMACS code. With an rpm the compiling etc has
>         > already been 
>         > done, so those .c files aren't needed.
>         > 
>         > If you want to gain access to the scripts and adjust them to
>         > your needs, I 
>         > suspect you will need to use the compiling version, so you
>         > have all the 
>         > source scripts/code/libraries etc.
>         > 
>         > Catch ya,
>         > 
>         > Dr. Dallas Warren
>         > Research Fellow
>         > Department of Pharmaceutical Biology and Pharmacology
>         > Victorian College of Pharmacy, Monash University
>         > 381 Royal Parade, Parkville VIC 3010
>         > dallas.warren at vcp.monash.edu.au
>         > +61 3 9903 9083
>         >
>         --------------------------------------------------------------------------
>         > When the only tool you own is a ha mmer, every problem
>         begins
>         > to resemble a nail.
>         > 
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>         > 
>         > 
>         > Xiaobing Tian Ph.D.
>         > Department of Microbiology and Immunology
>         > Thomas Jefferson University
>         > 1025 Walnut St., Suite 420
>         > Philadelphia, PA19107
>         > Phone: 215-955-1364 (Lab)
>         > 
>         > 
>         >
>         ______________________________________________________________________
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>         -- 
>         David.
>         ________________________________________________________________________
>         David van der Spoel, PhD, Assist. Prof., Molecular Biophysics
>         group,
>         Dept. of Cell and Molecular Biology, Uppsala University.
>         Husargatan 3, Box 596, 75124 Uppsala, Sweden
>         phone: 46 18 471 4205 fax: 46 18 511 755
>         spoel at xray.bmc.uu.se spoel at gromacs.org
>         http://xray.bmc.uu.se/~spoel
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> 
> 
> Xiaobing Tian Ph.D.
> Department of Microbiology and Immunology
> Thomas Jefferson University
> 1025 Walnut St., Suite 420
> Philadelphia, PA19107
> Phone: 215-955-1364 (Lab)
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! Finance Tax Center - File online. File on time.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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