VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Wed Mar 06 2024 - 09:36:55 CST

Hi Yixin,

How did you build your psf? The lipid atomtypes should be something like CTL2 or CTL3 or something if they are in the lipid tail, not C12 or C13. Somehow your atomtype field in the psf is populated with atomnames instead, which don’t match atomtypes in the parameter file that you loaded. If you started from the membrane builder tool in VMD, it is possible that you loaded the pdb first into VMD, which sets atomtypes by default based on the atomname. Then when you did the merger, it is possible that the correct atomtypes were not transferred.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Yixin Chen <yixin.chen1_at_ucdconnect.ie>
Date: Wednesday, March 6, 2024 at 10:08 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: looking for help to solve FATAL ERROR： Didn't find vdw parameter for atom type C11

Dear all,

I hope this email finds you well. I am looking for help regarding an error that occurred when I ran my simulation in NAMD. FATAL ERROR： Didn't find vdw parameter for atom type C11.

My simulation model comprises a graphene film and a lipid (POPC) membrane, both of which were constructed using the Carbon Nanostructure and Membrane Builder tools in VMD. I have combined these two components into a single PDB and PSF file. However, upon running the simulation, the aforementioned error arises. Upon reviewing the PDB file, I noticed that C11 (and similarly C12, C13, etc.) is part of the lipid membrane structure.

Initially, I thought that I might miss a parameter file, so I included all the necessary topology files in the configuration file. Despite this, the error persists. the parameter file I used is shown:
parameters par_all27_prot_lipid_na.inp
parameters par_all22_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_amber2charmm.inp

Additionally, I attempted to modify the atom designation from C11 to C in the PDB, PSF, and reference files, but the error message persists with a change in atom type (e.g., "Didn't find vdw parameter for atom type C12").

If anyone has encountered a similar issue or has expertise in troubleshooting NAMD simulations, I would greatly appreciate any insights or guidance you can provide. Thank you very much for your attention and help!

Best regards,
Yixin