[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

Justin Lemkul jalemkul at vt.edu
Mon Aug 21 00:02:25 CEST 2017

On 8/20/17 3:16 PM, Dilip H N wrote:
> Have you run pdb2gmx to process a simple protein or polypeptide? This is
> done for you.  Each amino acid is defined.  If you supply a coordinate file
> with a GLY-GLY peptide, pdb2gmx does everything you need.
> No Sir,  are thr any tutorials on polypeptide pdb generation and getting
> the topology (pdb2gmx process).., which would be highly beneficial....
> Thank you...

It's the simplest GROMACS use case.  Look through any of the tutorials linked on 
gromacs.org.  You need to have the starting coordinates already; GROMACS does 
not have the ability to generate a PDB of any arbitrary polypeptide for you.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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