Parameter and Topology Question - New NA Residues Alexander Corbet 11/30/22 01:23 PM
Hello, I'm hoping someone can clear up an issue that has arisen when trying to use charmm topology and parameters in NAMD/VMD.
I have been attempting to create xenosubstituted nucleic acids using amino acid side chains in place of normal nucleic acid bases. These are to be inserted in DNA sequences along with normal bases. To do this, I manually created topologies for these residues from the topologies of proteins and nucleic acids and was able to generate PSF files from these. I have also merged the protein and nucleic acid parameter files and included attachments with 'best guess' bond, angle, and dihedral values for the C1' to CB attachment. Unfortunately, while NAMD is able to run the simulation, the result is entirely nonsensical with bond features being entirely disrespected. Even the nucleic acid backbone is not immune to this distortion but only for the new residues (normal DNA behaves as expected). Given the modifications I've made I would expect the ribose sugar and the side chain to be maintained and the attachment between them to be suspect but not the entire residue. It's almost as if there's a call function that isn't reading these atoms because it doesn't recognise the residue names (which exist in the topology file and all resulting PSF and PDB files). The issue is occurring regardless of parameter files used (modified or not) and I am not receiving any error codes.
Using the latest topology and parameter files (36.1) with NAMD 2.14 Win64
Any chance anybody has any ideas on how to resolve this?
I've included images of the initial structure and of the structure after minimisation and a short dynamics run.
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