Simulating phosphoserine / phosphothreonine

GROMACS version:2022.2
GROMACS modification: Yes/No


I would like to add the TPO and SEP to the gromos54a7 forcefield. I updated the aminoacids.rtp, aminoacids.hdb, and atomtypes.atp files. I am using the syntax used in a previous build of GROMACS that included these modified amino acids in a FF.

2 questions:

  1. Do I need to alter any of the other files? For example: In the ffnonbonded.itp file, it specifies values for a number of “different types” of oxygens but “OP” (which is the oxygen on the phosphate group) is not mentioned. There is also no mention of “OP” in the ffbonded.itp file.

  2. Once I build the topology file locally, can I use that file to run the simulations on another computer that doesn’t have the modified aminoacids.rtp, aminoacids.hdb, and atomtypes.atp files? The assumption is that I will continue to use the gromos54a7 FF.

The reason being is that I don’t have permission to alter these files on the cluster I am using.

Thank you so much for your help.

Yes, any non-native parameters need to be added to the respective force field files, or otherwise defined in auxiliary files that are added with #include statements.

Those files only matter for pdb2gmx and then become irrelevant. If there are force field terms that aren’t defined, grompp will fail with a fatal error.

You can always work within a force field subdirectory in your working directory, or otherwise add necessary parameters to an .itp file in your home file system that you #include in your system topology.

I am getting errors indicating that it is treating the phosphorylated residues as OTHER. However, I cannot modify the residuetypes.dat file on the server.

Is there a link or reference on how to specify a local file for pdb2gmx to use when building the topology?



Make a copy in your local directory. All GROMACS programs read database files, force field directories, etc. from the working directory before looking in $GMXLIB.

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