Hi everyone!
I have a question about using charmm36 ff on gromacs. I copied the ff to my gromacs ff folder (opt) and I have been using it with no problem. Recently, I need to work with a protein containing non-standard residues, and others with glycosilation. I used CHARMM-GUI to apply those PTMs or non-standarad amino acids on my protein; However, when I use GROMACS and the same charmm36 ff, GROMACS shows me and error and says the CGU residue is not standard and it is not listed in residuetypes.dat file. I searched for this file and there is no such file in my charmm36.ff folder.
Does anybody know what can I do to fix this problem?
You should not need to use pdb2gmx
at all if you built the system with CHARMM-GUI; it provides all necessary GROMACS input files, including a topology.
Dealing with extensive PTMs is a major headache in GROMACS. It is much easier to handle these kinds of systems in CHARMM.
Thanks a lot for your response! Is there any way to learn charmm? is there a tutorial for its basics?
None that are particularly great, and none that will teach you everything you need to set up a system like this. But you don’t need one. CHARMM-GUI does it for you. As you said, you set up the system with PTMs with CHARMM-GUi. That should be the end of it. The server gives you everything you need to run GROMACS.