[gmx-users] Adding two peptides in a water box

[Sheyore Omovie]

Hi Luciano,
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.
Rgds
John
> Date: Sat, 8 Sep 2007 15:43:33 +0200> Subject: Re: [gmx-users] Adding two peptides in a water box> From: Lars.Schaefer at mpi-bpc.mpg.de> To: gmx-users at gromacs.org> > > Hi Everybory,> >> > I would like to simulate the interaction between two separated peptides in> > a water box. Every peptide needs to be N-and C-terminated. I have tried> > different alternatives in order to create the corresponding GROMACS files> > to start my simulation. I have used the GROMACS porograms tools as> > described in the manual. However, I still have some problems and need of> > your expeirences.> >> > This is what I do:> >> > 1.- I start from a pdb of one peptide.> > 2.- Create the gro and top files. In this step I terminate the peptide> > without any problem.> > 3.- Apply corresponding translations and rotation to the existing gro file> > (obtained in step 1) and create a new .gro file. This one is termed the> > second peptide.> > 4.- Cat them with an editor and save the result in a file named dimer.gro.> > I can visualize it without any problem. So far, everything is going good.> > 5.- HERE STARTS THE PROBLEM. I use dimer.gro as input to pdb2gmx to create> > the new, dimer.top file. The pdb2gmx removes the hydrogens of the N-term> > of one petide and the oxigen of the C-term in the second peptide.> > Although, they are far apart.> >> > Does anyone know how to overcome this porblem?> > Hi,> why do you run pdb2gmx for the dimer? run it for the monomer, and then> just put a "Protein 2" instead of a "Protein 1" (or however you name it)> at the end of your topol.top file (just as is done for the water> molecules, ions, etc).> Lars> >> > > Thank in advance for you time.> >> > Ciao,> >> > Luciano> >> > Dr. Luciano Triguero College of Art and Science Department of Physics and> > Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box> > 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:> > 305-284-3938> > _______________________________________________> > gmx-users mailing list gmx-users at gromacs.org> > http://www.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 gmx-users-request at gromacs.org.> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > > _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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