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<BR>Hi Luciano,<BR>
use the -label option to separately label the gro files (e.g A for the first peptide and B for the 2nd), before you cat them with an editor. pdb2gmx should now recognise them as separate molecules.<BR>
Rgds<BR>
John<BR>
<BR>> Date: Sat, 8 Sep 2007 15:43:33 +0200<BR>> Subject: Re: [gmx-users] Adding two peptides in a water box<BR>> From: Lars.Schaefer@mpi-bpc.mpg.de<BR>> To: gmx-users@gromacs.org<BR>> <BR>> > Hi Everybory,<BR>> ><BR>> > I would like to simulate the interaction between two separated peptides in<BR>> > a water box. Every peptide needs to be N-and C-terminated. I have tried<BR>> > different alternatives in order to create the corresponding GROMACS files<BR>> > to start my simulation. I have used the GROMACS porograms tools as<BR>> > described in the manual. However, I still have some problems and need of<BR>> > your expeirences.<BR>> ><BR>> > This is what I do:<BR>> ><BR>> > 1.- I start from a pdb of one peptide.<BR>> > 2.- Create the gro and top files. In this step I terminate the peptide<BR>> > without any problem.<BR>> > 3.- Apply corresponding translations and rotation to the existing gro file<BR>> > (obtained in step 1) and create a new .gro file. This one is termed the<BR>> > second peptide.<BR>> > 4.- Cat them with an editor and save the result in a file named dimer.gro.<BR>> > I can visualize it without any problem. So far, everything is going good.<BR>> > 5.- HERE STARTS THE PROBLEM. I use dimer.gro as input to pdb2gmx to create<BR>> > the new, dimer.top file. The pdb2gmx removes the hydrogens of the N-term<BR>> > of one petide and the oxigen of the C-term in the second peptide.<BR>> > Although, they are far apart.<BR>> ><BR>> > Does anyone know how to overcome this porblem?<BR>> <BR>> Hi,<BR>> why do you run pdb2gmx for the dimer? run it for the monomer, and then<BR>> just put a "Protein 2" instead of a "Protein 1" (or however you name it)<BR>> at the end of your topol.top file (just as is done for the water<BR>> molecules, ions, etc).<BR>> Lars<BR>> ><BR>> <BR>> > Thank in advance for you time.<BR>> ><BR>> > Ciao,<BR>> ><BR>> > Luciano<BR>> ><BR>> > Dr. Luciano Triguero College of Art and Science Department of Physics and<BR>> > Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box<BR>> > 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:<BR>> > 305-284-3938<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>> <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 />Make your little one a shining star! <a href='http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us' target='_new'>Shine on!</a></body>
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