Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them??
Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli < [email protected]> wrote: > Hi, > > If I understood your question, do you want to know how can you start a > simulation? So, if I'm correct I recommend this link > http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this > link, there is flowsheet file which is the flowchart to Gromacs simulation. > > Answered your question a little more specific, although basically, after > you get the pdb file, you need to run the pdb2gmx program. The link above > explains more details about it. > > I hope that this email helped you. > > Cheers, > > -- > Rodrigo Antonio Faccioli > Ph.D Student in Electrical Engineering > University of Sao Paulo - USP > Engineering School of Sao Carlos - EESC > Department of Electrical Engineering - SEL > Intelligent System in Structure Bioinformatics > http://laips.sel.eesc.usp.br > Phone: 55 (16) 3373-9366 Ext 229 > Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 > > > On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed <[email protected]>wrote: > >> Hi, >> >> I have a basic question (since I am new). For starting any simulation as I >> understand, is to find a .pdb or .gor file. Pdb files for proteins are >> already there, but for a new system what is the easiest and quick way to >> find it (which software etc). What about .gro files????? >> >> >> >> I appreciate your help for solve my basic problems. >> >> Thanks, Jamie >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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