I am learning NAMD for simulating membrane embedded proteins. While running simulation, can we use different versions of Charmm parameter files?
Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON3", is coming, but there are no ON3 atoms in my structure. For running this simulation, I have used parameter files as mentioned below:
parameters par_all36_lipid.prm
parameters par_all36m_prot.prm
parameters toppar_water_ions.str
In a single simulation, it is not recommended to use two different versions of CHARMM files as the some of the parameters may change in the new version. And if you are using the files from different version, you may get the newer parameter for one atom but older parameter for another atom.
Regarding the error, please check in your psf file that you have any ON3 type of atom or not. If ON3 atoms are not present in the pdb but present in the psf then this error can occur.
Thanks for the suggestion @Imon Mandal. I have checked both pdb and psf file and atom ON3 is in neither.
Hi,
I am getting the same error "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON3." There is no ON3 atom in the pdb and psf files.
Any solution how to troubleshoot this?
- Badges
- Science topic
- Similar topics
- Engineering
- Chemical Engineering
- Membranes