[gmx-users] How to edit the specbond.dat file? Again
xiaobingtian at yahoo.com
Tue Mar 30 17:07:04 CEST 2004
I am a beginner in the field. I looked up the protein.pdb and protein.gro files. Still I could not find where i can put the value (0.2 nm +/- 10) in those files. In addition, I have installed .rpm files of Linux version 3.2.1. I have tried hard to find the specbond.c file. But the computer showed that it can not find it at /root or /usr directories.
Is it possible that you kindly give me a more detailed instructions?
Thank you very much for your time and patience!
David <spoel at xray.bmc.uu.se> wrote:
On Mon, 2004-03-29 at 23:42, xiaobing tian wrote:
> Hi David,
> I appreciated your replies.
> The following is the specbond.dat file. I don't know where I should
> edit the tolerance.
Good point, it isn't there! Oops, in that case you have to somehow take
care that these Cys residues are at the correct distance (0.2 nm +/- 10
%) in the coordinate file.
Alternatively you can edit the source code in src/kernel/specbond.c,
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> CYS SG 1 HEME FE 2 0.25 CYS2 HEME
> CYS SG 1 HEME CAB 1 0.2 CYS2 HEME
> CYS SG 1 HEME CAC 1 0.2 CYS2 HEME
> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
> 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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Xiaobing Tian Ph.D.
Department of Microbiology and Immunology
Thomas Jefferson University
1025 Walnut St., Suite 420
Phone: 215-955-1364 (Lab)
Do you Yahoo!?
Yahoo! Finance Tax Center - File online. File on time.
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