[gmx-users] Simulation of D-Alanine

prasun kumar prasun30 at gmail.com
Fri Mar 16 11:07:53 CET 2018

Hi Group:

I am trying to simulate a peptide containing D-Alanine (DAL). For this
purpose, I am using Charmm36m Force Field.
While running the command 'pdb2gmx -f input.pdb -ignh -ff charmm36-july17',
I got an error saying 'DAL is not defined' (something similar to this). I
understand that the residue name DAL is not given in the merged.rtp file.
However, DALA is present. Keeping the nomenclature in mind, I added a line
"DAL       DALA" in merged.r2b file. Now my command is running, but  it is
not able to add hydrogen atoms to DAL residues.

Please guide me.

Thank You in advance

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Resolution + Hard work = Success

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