[gmx-developers] Dummy mass missing in OPLS

Ondrej Marsalek ondrej.marsalek at gmail.com
Thu Nov 5 14:06:39 CET 2009


I am trying to use virtual sites for hydrogens with OPLS and ACE...NAC
terminated peptides. The CH3 in ACE is processed fine, bot the one in
NAC is not. I got the following error from pdb2gmx:

Cant find dummy mass (in ffoplsaa.ddb) for type opls_242 bonded to
type opls_238. Add it to the database!

After looking at the instructions in the ffoplsaa.ddb file, it looks
like the right resolution is to add in the CH3 section the following

   opls_242  opls_238   MCH3A

I have added this in my own installation, but could this please be
added to the distribution? This is on GROMACS 4.0.5.

Ondrej Marsalek

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