[gmx-users] modified atomtypes.atp and grompp

Rausch, Felix frausch at ipb-halle.de
Fri Mar 11 08:08:29 CET 2011

Dear Gromacs users,
I would like so simulate a protein with phosphorylated amino acids with Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from the user contributions section (subsection force fields) and adapted the parameters given there to Gromos53a6. 
The problem now is that they introduced a new atom type called "OP", which I have to add to the atomtypes.atp of my modified force field. I already read about problems of a modified atomtypes.atp here in the mailing list, but I assumed the problems were sorted out with version 4.5.3.
But if I add OP to the atom list, pdb2gmx works fine, but grompp is raising the error
Program grompp, VERSION 4.5.3.
Source code file: toppush.c, line: 629
Fatal error:
Unknown atomtype CMET
which is quite strange because  "CMET" isn't appearing in any file I'm using. When I remove OP from the atom list, pdb2gmx is of course raising an error, so I'm a bit stuck here...
To cut a long story short: Is there any way to introduce a new atom type to atomtypes.atp or do I have to parameterize the phosphorylated residues with already presend atom types?  
Thank you in advance,
Felix Rausch


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