Hi All,<br><br> I am trying to put 2 identical peptide chains in a simulation box. However, gromacs tends to see both separate peptide chains as one. <br><br> The following is the method that I used, please comment and correct me if I'm wrong.
<br><br> 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.
<br><br> 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.
<br><br> 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.
<br><br> Many thanks. <br> <br clear="all"><br>-- <br>Best regards,<br>Huey Ling