[gmx-users] Regarding naming dipeptide in charmm36 Forcefield
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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