<DIV>Dear David,</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV>Is it possible that you kindly give me a more detailed instructions?</DIV>
<DIV> </DIV>
<DIV>Thank you very much for your time and patience!</DIV>
<DIV> </DIV>
<DIV> Sincerely,</DIV>
<DIV> </DIV>
<DIV>Xiaobing<BR><BR><B><I>David <spoel@xray.bmc.uu.se></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">On Mon, 2004-03-29 at 23:42, xiaobing tian wrote:<BR>> Hi David,<BR>> <BR>> I appreciated your replies.<BR>> The following is the specbond.dat file. I don't know where I should<BR>> edit the tolerance.<BR>Good point, it isn't there! Oops, in that case you have to somehow take<BR>care that these Cys residues are at the correct distance (0.2 nm +/- 10<BR>%) in the coordinate file.<BR><BR>Alternatively you can edit the source code in src/kernel/specbond.c,<BR>routine is_bond<BR><BR><BR>> <BR>> 5<BR>> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2<BR>> CYS SG 1 HEME FE 2 0.25 CYS2 HEME<BR>> CYS SG 1 HEME CAB 1 0.2 CYS2 HEME<BR>> CYS SG 1 HEME CAC 1 0.2 CYS2 HEME<BR>> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME<BR>> <BR>> Thanks,<BR>> <BR>> Xiaobing<BR>> <BR>> Xiaobing Tian Ph.D.<BR>> Department of Microbiology and Immunology<BR>> Thomas Jefferson
University<BR>> 1025 Walnut St., Suite 420<BR>> Philadelphia, PA19107<BR>> Phone: 215-955-1364 (Lab)<BR>> <BR>> <BR>> ______________________________________________________________________<BR>> Do you Yahoo!?<BR>> Yahoo! Finance Tax Center - File online. File on time.<BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,<BR>Dept. of Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www
interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE><BR><BR>Xiaobing Tian Ph.D.<br>Department of Microbiology and Immunology<br>Thomas Jefferson University<br>1025 Walnut St., Suite 420<br>Philadelphia, PA19107<br>Phone: 215-955-1364 (Lab)<p><hr size=1><font face=arial size=-1>Do you Yahoo!?<br>
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