It has a massive SI which has all kinds of information but I cannot seem to find the final parameters for these amino acids. Is there a source where the actual parameters can be obtained?
Thank you in advance. I apologize that this is not a GROMACS question but I hope that enough people are using CHARMM36 with GROMACS (courtesy of the MacKerell port) that this will be of interest.
Best wishes,
Gregory
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All the associated parameters are in the CHARMM toppar distribution (the stream/prot/toppar_all36_prot_modify_res.str file) and have been included in the latest CHARMM36 port for GROMACS. Everything is in there as of the July 2022 port.
Many thanks for the pointer. I was able to find non-natural amino acids dispersed in the aminoacids.rtp file. My luck will have it that the chloro-substituted amino acids, which are the ones I am looking for specifically, are not in the port. In the toppar files, the Cl- (and Br-) substituents have an additional LP1 atom attached to them. I found out (from googling) that they represent lone pairs. Could I get your recommendation on what to do here? I could duplicate and adapt a similar entry in the .rtp file, but should I create a virtual/fake atom in the pdb for LP1? Or just add the (relative small) LP1 charge to the Cl atom? Or something else?
The issue is that pdb2gmx has no ability to generate the kind of lone pairs that are necessary to represent σ hole effects on halogens. These are really important for modeling halogen bonding. Because of this technical problem, we omit residues that have lone pairs in them when converting the force field. There is not an easy solution to this that I can think of.