Hello Huey Ling, Use different chain identifiers for different peptides.
Then pdb2gmx will not create any bond between them. Regards, Alok > Hi All, > > I am trying to put 2 identical peptide chains in a simulation box. > However, gromacs tends to see both separate peptide chains as one. > > The following is the method that I used, please comment and correct me > if > I'm wrong. > > First, I translate the peptide to a certain distance. Then I put the > .gro > files of the translated peptide in the first .gro file. Later, I change > the > number of the residues and atoms of the second peptide accordingly and > manually. > > With the .gro file of the 2 peptide chains, I convert it to pdb file. > And > then, I use the pdb2mgx to convert the 2peptide.pdb to 2peptide.gro to > generate topology file. The rest of the methods are the conventional > gromacs > simulations such as energy minimisation and position restrained. > > However, gromacs see the 2peptide.pdb file as a file for 1 single > molecule, (not 2 identical peptide chains in a file) and bond is created > between this 2 chains. I tried to use -nmol to insert the second peptide > in > but that doesn't work. I wonder if anyone have done similar work like mine > before, and willing to share the method with me? Any other suggestion and > comments are most welcome. > > Many thanks. > > > -- > Best regards, > Huey Ling > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
