Hi I am working on simulating lipid bilayers with previtamin D. I have generated a CMAP for the open-ring portion of the previtamin D molecule and I want to apply it to my system.
The membrane contains a total of eight Pre molecules and I am unsure how to get the CMAP to apply to all the molecules and not just RESID 1. My assumption is that the !NCRTERM portion of step5_assembly.psf requires one line for each dihedral that will be modified by the CMAP, with the atom types identified in my ligand rtf file. If I have eight ligands then I should have eight lines.
The CHARMM output states that the additional cross-terms that I have defined do not have an associated CMAP. My confusion stems from the fact that the atoms I selected in the !NCRTERM block do not correspond to the same types shown in output. I used the atom indices from the psf file to select the atoms and in that file they have the correct type.
Ultimately what I am looking to find out is this: do I need a new cross-term for each separate ligand or will CHARMM recognize one cross-term and apply it to the other ligands for me? (Handling multiple cross-terms is not discussed in the prm portion of the user manual)
I have attached four files: the output from my attempted run, the coordinates and cross-term blocks from step5_assembly.psf (full file too large), and the rtf and prm file for my previtamin D ligand.
Also, below is a highlight showing how the atom labels are not corresponding with what I am expecting.