[gmx-users] 15-20% tolerance?
spoel at xray.bmc.uu.se
Wed Mar 31 19:22:01 CEST 2004
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.
> 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?
> But you can still edit your coordinate file such that the
> 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
> > 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
> > 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)
> > Do you Yahoo!?
> > Yahoo! Finance Tax Center - File online. File on time.
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics
> 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
> gmx-users mailing list
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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 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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