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Hello, I’m currently working on a molecular dynamics simulation of a glycosylated protein using GROMACS 2022/7 with the CHARMM36 force field. I imported the parameters of the sugar (2-acetamido-2-deoxy-beta-D-glucopyranose) using CHARMM-GUI. The issue I’m encountering is that the oxygen atom on carbon 1 in the sugar ring is missing among the residue atoms in the PDB file. This oxygen in the sugar chain is replaced by the oxygen on C4 of the preceding residue. Consequently, when compiling the .hdb file for this sugar, I cannot provide a 4th reference atom for C1, as this carbon is only bonded to two other non-hydrogen atoms. I’m unable to describe H1 as a tetrahedral atom due to this missing third atom. I’ve attempted to use the “5” method of adding hydrogen, but the dihedral is incorrect, and the result is as pictured below. Thank you in advance for any assistance.
Could you clarify a bit? Is the problem that the input PDB file is missing atoms? Or are they just misplaced in the file, and the residue naming? If you know where they should be (approximate coordinates) you could add them by hand in the PDB file. If they are just assigned to the wrong residue you should be able to manage that in the PDB file as well. There might be other ways to solve this, but if the PDB file is not correct then you will probably have to fix it, one way or another.
There were no missing atoms in the PDB file, except for the hydrogens as usual. The problem arose during the assignment of hydrogens when creating the GRO file. I wrote how to assign hydrogens to each individual sugar residue in the HDB file. However, in the HDB file, all reference atoms must be from the same residue to which the hydrogen belongs. Nevertheless, in the formation of the glycosidic bond, one of the oxygens is necessarily missing, and the remaining oxygen is from the first sugar of the two sugars forming the glycosidic bond. Therefore, I couldn’t define the hydrogen bonded to the carbon as a single tetrahedral hydrogen since the oxygen that would have been the fourth reference atom was missing. I avoided this problem by merging the amino acid and the entire sugar chain into a single residue—an Asn with 4 sugar units- in the pdb, hdb and itp files. Would there have been a more straightforward method? I apologize if I was unclear.
