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.
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