[gmx-users] Simulation of D-Alanine (prasun kumar)

ABEL Stephane Stephane.ABEL at cea.fr
Fri Mar 16 12:08:07 CET 2018


I added the same problems few days ago.There is no hdb entries for D-AA, so GROMACS can not generate the missing Hs. So I would suggest you to use CHARMM-GUI, instead and use a fake *.itp with the L-ALA (ALA) renamed to DALA. 

Good luck



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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