[gmx-users] regarding "-missing" option of pdb2gmx

Мижээ Батсайхан b.mijiddorj at gmail.com
Mon Feb 5 07:57:43 CET 2018

Dear gmx users,

I want to perform MD simulations of D-amino acid containing protein, and
force field is charmm36, last version, which contains the parameters of
D-amino acids. When I use pdb2gmx, I received following error:

Fatal error:
There were 10 missing atoms in molecule Protein, if you want to use this
incomplete topology anyhow, use the option -missing

My questions:
1. Can I use above -missing option for pdb2gmx?
2. What is the effect in the results in case of using the incomplete

Best regards,


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