VMD-L Mailing List

From: Yixin Chen (yixin.chen1_at_ucdconnect.ie)
Date: Wed Mar 06 2024 - 08:12:31 CST

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