[gmx-users] How to edit the specbond.dat file? Again

[xiaobing tian]

Dear David,
 
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!
 
 Sincerely,
 
Xiaobing

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,
routine is_bond


> 
> 5
> 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
> 
> Thanks,
> 
> Xiaobing
> 
> 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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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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