Hello there,
Is there anyway one can generate all the residues in mutres.mtp and mutres.rtp file of all the residues that are present in the force field including cgenff residues that are included in CHARMM36-Jul2021?
Moreover, I would also want to know about generating hybrid ligand topologies.
Regards,
Pallav
Hey Pallav,
“pmx genlib” can be used to generate amino acid mutation residue databases. It will work with the canonical amino acids, thus not all the cgenff entries will be understood.
To generate ligand hybrid structures/topologies use “pmx atomMapping” to identify atom mapping between the two ligands and afterwards run “pmx ligandHybrid” to create the actual morph.
Vytas
Is there anyway we can work with modified nucleotides apart from the fact that you have a library for the same?
Arbitrary covalent modifications are not currently supported. You would need to either rely on the existing mutation libraries or treat the modification as a ligand and later add the required covalent bonded parameters.
Vytas