I have created coordinate and psf files for my system comprising of a modified nucleic acid inside a protein, embedded in a lipid (step5_input.pdb/psf/crd) using CHARMM-GUI. However, I would like to add one triple bond between atom# 22424 and 23769 and also obtain the updated PSF and CRD files. The bond is supposed to be created between C5M of THY 17 and C1 of DL 61 which is the modification created using CGenff. My understanding is that one cannot use just CHARMM-GUI to create non-covalent bond between a biomolecular and a non-biomolecular part. Is that true? After I get the output from CHARMM-GUI I dont see any bond between those two although (absent from step5_input.psf) I made sure that CONECT records were there in the input PDB. Now, with this PDD+PSF I want to incorporate the triple bond, update the angle, dihedral etc info in a new PSF and CRD files and submit them to CHARMM-GUI FF-Converter for creating my system correctly. I have limited experience with PSFGEN tools and that's why I am asking for your help. If you can provide me with some help on how to write a sample psfgen script with my system for the triple covalent bond that I am looking for that would be of tremendous help. I am not sure what my PATCH statement would be for PSFGEN to work. You may find the associated files in the attached link. The FF parameters are in the toppar directory.https://drive.google.com/drive/folders/1zY_zfwIzDgNGJiqxdGAaWSc40un6m7V2
I would be grateful if you share your thoughts on this approach of modelling a modified nucleic acid using CHARMM-GUI. If CHARMM-GUI is not adequate I need to use updated versions of my PSF/CRD files and I would like to have your help with PSFGEN or some other way.
Thank you !