<DIV>Dear David,</DIV>
<DIV> </DIV>
<DIV>I just specified the flag -cys. But pdb2gmx showed "unknown argument -cys"</DIV>
<DIV>Then i tried flag -ss, it resulted wrong bonds that containd carbon atoms and were </DIV>
<DIV>protonated. What were wrong with that?</DIV>
<DIV> </DIV>
<DIV>Thanks again,</DIV>
<DIV> </DIV>
<DIV>Xiaobing Tian<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 21:43, xiaobing tian wrote:<BR>> <BR>> Dear Gromacs users,<BR>> <BR>> <BR>> <BR>> I made a position-restrained MD simulation with protein 1AZ8. The<BR>> simulation terminated prematurely due to a bunch of Lincs Warnings (<BR>> started about from the steps 5000). <BR>> <BR><BR>you have to check when running pdb2gmx whether all disulfide bonds are<BR>made. if not you need to specify a flag -cys to make the bonds<BR>interactively.<BR>> <BR>> <BR>> When I prepared the protein PDB file, I deleted the drug that bound to<BR>> it and water molecules. I have kept the CONNETCTIONs for disulfide<BR>> bonds on the PDB file. The six disulfide bonds of the protein were<BR>> correctly displayed on Rasmol, PDB viewer and AutoDock Tool. But when<BR>> I used VMD to check the file, the four disulfide bridges among the six<BR>> were
missing in the PDB file. I was able to produce .top and .gro<BR>> files with pdb2gmx (v. 3.2.1), using Gromacs force field, and go on<BR>> the MD simulation till the Lincs Warnigs occurred.<BR>> <BR>> <BR>> <BR>> I have checked the .gro file produced from pdb2gmx and other .gro<BR>> files by VMD, all of them showed several abnormal and wrong bonds or<BR>> atom groups formed between those disulfide atoms. Is this the cause<BR>> that resulted in Lincs Warnings and premature termination of MD? How<BR>> to fix this problems?<BR>> <BR>> <BR>> <BR>> Thank you very much in advance.<BR>> <BR>> <BR>> <BR>> Xiaobing Tian<BR>> <BR>> <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>
<a href="http://taxes.yahoo.com/filing.html"><b>Yahoo! Finance Tax Center</a></b> - File online. File on time.