[gmx-users] Dihedral calculations in topology

Kamps, M. m.kamps at student.rug.nl
Wed Dec 21 15:21:45 CET 2016


Thanks again for the swift reply! Stupid of me to miss that message! I
noticed some other code that was generated as output of pdb2gmx, which
I do not fully understand. Can you maybe explain some of it?

Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.

I understand the two warnings. To my directory I added a file
residuetypes.dat, where I specificy that (among others) EthB and EthE
(which are the ending and beginning residues of polyethylene) are
Polymer. What does the rest of this message mean? I don't understand
how I could fix this message? Or even what it wants to do, since i've
defined my own terminal residues. Is it not possible to define my own

EthB    Polymer
EthE    Polymer


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