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

alokjain at iitk.ac.in alokjain at iitk.ac.in
Fri Oct 26 20:39:41 CEST 2007

Hello Huey Ling,

Use different chain identifiers for different peptides.

Then pdb2gmx will not create  any bond between them.


> 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
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