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

[Huey Ling Tan]

Hi Alok,

   Thanks for your email.

   Could you please explain in more detail? What do you mean by chain
identifier?

   Many thanks.

Best regards,
Huey Ling

On 26/10/2007, alokjain at iitk.ac.in <alokjain at iitk.ac.in> wrote:
>
> Hello Huey Ling,
>
> Use different chain identifiers for different peptides.
>
> Then pdb2gmx will not create  any bond between them.
>
> Regards,
> Alok
>
>
> > 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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