[gmx-users] Regarding naming dipeptide in charmm36 Forcefield

[Justin Lemkul]

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

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================