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

[Justin A. Lemkul]

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
proteins.

So your [ molecules ] section would go from:

[ molecules ]
Protein     1

to

[ molecules ]
Protein     2

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

-Justin



======================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

======================