[gmx-users] Adding two peptides in a water box

[Mark Abraham]

> Hi,
> why do you run pdb2gmx for the dimer? run it for the monomer, and then
> just put a "Protein 2" instead of a "Protein 1" (or however you name it)
> at the end of your topol.top file (just as is done for the water
> molecules, ions, etc).
> Lars

Clarifying, if the two peptides are identical, then all you need to do is
edit the [ molecules ] section of the .top file you got the first time to
indicate that there are two of them. Now the modified .gro will work with
the modified .top file, and you can go and solvate, etc.

Having read chapter five of the manual might have suggested this solution
to you...

Also, reading pdb2gmx -h would have found you another solution, because
there's an option to pdb2gmx that allows you to generate separate
topologies for separate chains in the structure file. This is a more
general solution when the peptides are not identical.

Mark