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.
Thank you for the quick response Rick. So if I am understanding correctly, I only need the first definition for the cross-terms block in the psf file and CHARMM will apply that to the other 7 Pre molecules.
I changed the terminal command in the prm file from stop to end as you suggested and the warning disappeared. Thanks for catching that!!
I am still getting the missing cross-term map error, only for some reason it is declaring a different set of atom types than in the original error message, even though the atom selections were the same:
Is it possible for me to use the .prm and .rtf files from my original system, which already contain the CMAP stub and the dihedral definition, and load them manually during Step 1 of the Membrane Builder instead of generating new files? My hope is that CHARMM will automatically include the cross-terms in the Step5_assembly.psf file and use the correct atom typing. I would just cut that block and paste it into the psf for the original system.
Manual modification of a PSF is usually a bad idea.
Yes this is where I was having trouble. I had underestimated the sensitivity of the psf file when I was adding my cross-terms. The alignment of the numbers is apparently significant and I was not aware of this. I had been trying to keep the same quantity of delimited spaces between each column instead of trying to keep the numbers in the columns aligned.
I attached an image of the correct alignment that I am now using.
This was not very apparent in my OP as the forum reformatted the text in the !NCRTERM block, though it is visible at the bottom of psf.txt file... but this made all the difference. CHARMM no longer crashes with the MISSING PARAMETERS error.
Thank you @rmv for your help.
Last edited by ASmittie; 08/31/2111:17 PM. Reason: clarity