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

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 26 17:43:58 CEST 2007

Quoting Huey Ling Tan <huelyn at gmail.com>:

> 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

I would recommend processing one peptide structure with pdb2gmx, and then
changing your [ molecules ] section in the output topol.top to include 2

So your [ molecules ] section would go from:

[ molecules ]
Protein     1


[ molecules ]
Protein     2

After you've done that, then create your system with two peptides in it, using
this topology.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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