[gmx-users] Problem putting 2 identical peptide chains in a simulation box

Huey Ling Tan huelyn at gmail.com
Fri Oct 26 17:03:02 CEST 2007

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

   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
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