[gmx-users] protein peptide interaction -reg

Justin Lemkul jalemkul at vt.edu
Mon Oct 1 14:56:56 CEST 2012

On 10/1/12 8:52 AM, venkatesh s wrote:
> Respected Gromacs Users,
>                                   i am trying to simulate protein peptide
> want understand interaction
> my protien 210 Amino acid and my peptide only 5 Amino acid, and molecular
> types different (between protein peptide )
> docked conformation  (may i follow Protein ligand tutorial )

No.  You should process the peptide ligand with pdb2gmx, not any external 
topology producing sites.

> inserting peptide into pdb file
> or
> which suitable way i want do in gromacs ?

Either will work.  The syntax of the coordinate file is all that matters. 
pdb2gmx can handle multiple proteins in the same file, provided they are 
separated by TER or have different chain identifiers.  pdb2gmx should then 
produce two topologies (.itp files), one for each protein (the larger protein 
and the peptide ligand).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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