[gmx-users] Whics is correct coordinate file for enditing?
spoel at xray.bmc.uu.se
Wed Mar 31 20:23:01 CEST 2004
On Wed, 2004-03-31 at 19:57, xiaobing tian wrote:
> Hi David,
> Thank you for your reply.
> First of all, I tried to edit coordinate file, such as 1az8.pdb and
> 1az8.gro files. Unfortunately, there are not any values of bond length
> listed in those files.
> Did I choose wrong files?
you have to edit the coordinates and compute the bondlengths on a piece
> Thanks again,
> David <spoel at xray.bmc.uu.se> wrote:
> 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 wrote:
> > On Wed, 2004-03-31 at 16:51, xiaobing tian wrote:
> 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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