I've been trying to install this new ffG54a7 GROMACS force field for post-translational modifications : http://vienna-ptm.univie.ac.at/?page_id=100
I copied the downloaded folder into the "gromacs_installation/share/top" folder, and the force field seems to be installed fine since it appears on the list of available force fields when I use pdb2gmx, and it can be used and works without crashing for standard sequences.
However, whenever I use it on a sequence that has, say, a Y2P residue (which is a phosphorylated tyrosine), from a PDB file generated by the PTM tool on their website, I get a
Fatal error: Residue 'Y2P' not found in residue topology database
So I went to check the .rtp files, and there exists a Y2P entry in the gromos54a7.ff/aminoacids.rtp file. There also is one in the aminoacids.dat and residuetypes.dat files in the same directory.
I contacted the forcefield team and they can't see where the problem comes from. I tried with Gromacs 4.6.3 and 4.6.7, on two local computers and a cluster and get the same problem.
Is there something I'm not seeing ?
Thanks!
If you make a slight change in your .rtp file in the working case, does it affect the resulting topology? This way you can make sure that your pdb2gmx recognizes the right .rtp.
For me, the most plausible source of your error is that the file residuetypes.dat should be in the *parent* directory (that is, .../share/gromacs/top) and not in the .ff directory. They might have put it in the .ff folder to avoid overwriting any pre-existing custom version of the file, and apparently assumed that you'll mv it by yourself.
Maybe you are missing the flag (-ff forcefeildfoldername) in pdb2gmx command to read your modified forcefeild if you have the ff folder in your working directory
i.e. pdb2gmx -f test.pdb -ff ffG54a7 -o protein.gro -p protein.top -o output.pdb
Roman Sarrazin-Gendron How did you fix this issue? In my case if I invoke the pdb2gmx command, the force field does not appear in the list! However, if I paste the folder of the force field in the working directory and I use the -ff flag the force field is recognized but I get the same error as you. I would like to do some MD simulations with acetylated lysines. How did you end up doing your simulations on Gromacs with your protein bearing the PTMs? Regards,
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