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

[ABEL Stephane]

Hi 

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

Stéphane 

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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
Prasun

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success


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