Hi guys! I have a GROMACS port of a cetrain CHARMM force field (say, charmXX.ff). It contains topologies for all canonical amino acids and also nucleotides. Now, I've got PDB of a protein that has GTP or GDP (+Mg) in its active site.
I've constructed GTP/GDP topologies by combining the adenosine groups of ATP/ADP and guanosine. This worked well. But I still have these topologies in the CHARMM format (like top_allXX_na_nad_ppi.str).
My question is - how can I now "embed" these CHARMM topologies into my GROMACS port charmXX.ff?
Thanks a lot in advance!
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
It's the same operation you did in CHARMM format, just do it in the GROMACS .rtp file instead so that pdb2gmx can process it.
Hi Justin, thanks for you answer. I have another question:
in the GROMACS port, I have 4 different *.rtp files (aminoacids.rtp, dna.rtp, lipids.rtp, rna.rtp). GTP/GDP do not really belong to any of these groups. Is it important to have my new entry in a particular *.rtp file?
No, it's completely irrelevant. pdb2gmx reads any and all .rtp files it finds.
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