From: Monika Kumari (Monika.Kumari_at_chemistry.iitd.ac.in)
Date: Wed Nov 30 2022 - 03:15:59 CST
The error clearly mentions that the parameter file you provided doesn't
contain all the parameters needed to run the calculation. A safe option
is to provide all the parameter files you considered while running the
original simulation using namd3. The plugin can take multiple parameter
files separated by (I think) a space.
Best,
Monika
-------- Original Message --------
Subject: namd-l: The parameter error in the NAMD Energy of VMD
Date: 29.11.2022 23:32
From: Rulong Ma <rulong.ma.jlu_at_gmail.com>
To: namd-l_at_ks.uiuc.edu
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?
-- Best, Rulong Ma CAUTION: This email originated from outside of IIT Delhi. Do not click links or open attachments unless you recognize the sender and know the content is safe.
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