From: Rulong Ma (rulong.ma.jlu_at_gmail.com)
Date: Tue Nov 29 2022 - 12:02:19 CST
Hi the teams of NAMD and VMD.
There is a parameter error in the NAMD Energy of VMD when I calculated the
interaction energy between protein and RNA.
The NAMD3 was used to run protein-RNA simulation. However, NAMD Energy
needs namd2 for energy calculation.
The setting is shown in the following figure. The parameter file is
"par_all36m_prot.prm". However, after running NAMD energy, there was an
error. "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN5". But I
did not find "ATOM HN5" in my simulation system.
when the parameter file is "par_all36_na.prm". There is another error, "
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NH3 ". I did not find
"ATOM NH3" in my simulation system.
If I did not choose a parameter file, There is another error, " FATAL
ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1 ". But " ATOM HB1" is
the atom of Methionine.
Would you help to solve this problem?
[image: image.png]
-- Best, Rulong Ma
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST