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I have used pymol to generate pdb files for simple polypeptides.<BR>
You might want to check to see if it will meet your needs.<BR>
Rgds<BR>
John<BR><BR>> From: shura@phys.sinica.edu.tw<BR>> To: gmx-users@gromacs.org<BR>> Date: Fri, 24 Aug 2007 07:48:27 +0800<BR>> Subject: [gmx-users] generation of the pdb file<BR>> <BR>> <BR>> Hi,<BR>> I am new in GROMACS and MD though have some experience of MM and Monte Carlo<BR>> simulations. I have looked through the users archive as carefully as I could<BR>> but couldn't find the answer to my (probably very simple) question: <BR>> how to generate pdb file if your peptide is not in PDB databank? T.e. suppose<BR>> I know only the aminoacid sequence and want to do a folding simulation or<BR>> simulated annealing starting from some random conformation. Then how to<BR>> generate a pdf file for GROMACS? Thanks.<BR>> <BR>> Shura<BR>> <BR>> --<BR>> Open WebMail Project (http://www.phys.sinica.edu.tw)<BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<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.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><br /><hr />Find a local pizza place, movie theater, and more….then map the best route! <a href='http://maps.live.com/default.aspx?v=2&ss=yp.bars~yp.pizza~yp.movie%20theater&cp=42.358996~-71.056691&style=r&lvl=13&tilt=-90&dir=0&alt=-1000&scene=950607&encType=1&FORM=MGAC01' target='_new'>Find it!</a></body>
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