Specifying a pull direction with COLVARS

From: Selemon Bekele (selemon_at_uakron.edu)
Date: Mon May 25 2020 - 23:52:47 CDT

Hi there,

   I am trying to run a pulling simulation using the COLVARS module in NAMD (version 2.13). This is my first time to use COLVARS and am still learning about it.

The goal is to pull an ion from its binding pocket in a protein. I want to specify a pull direction by scanning the distances between the ion and the center of mass of the coordinating atoms, the polar angle (polarTheta) and the azimutal angle (polarPhi) in a coordinate system centered on the center of mass. I need the protein RMSD to be restrained.

  Simulations with a simple distance colvars run fine. However, when I try to include the angles, the simulation fails. I have attached the necessary files if anyone can spot what I am doing wrong. All files referenced in the input scripts have been used before and have no issues. May be the input structure is not compatible with the version of COLVARS in the NAMD version I am using. I am not sure why it works for a simple distance colvars though. A simulation with only polarPhi or polarTheta also fails with the same error message which is shown below.

TCL: parameter unknown for NAMD config parameter
FATAL ERROR: parameter unknown for NAMD config parameter
    while executing
    invoked from within
"cv config "

# This string is not Tcl code, but you can still use in here Tcl variables,
# such as ${numsteps}, and bracket expansion, such as [output..."
    (file "drag_3d.namd" line 5)
    invoked from within
"source drag_3d.namd "
    (file "smd_s0.namd" line 128)
[0] Stack Traceback:
  [0:0] CmiAbortHelper+0x6b [0xdd761b]
  [0:1] _Z8NAMD_diePKc+0x70 [0x64ceb0]
  [0:2] _Z18after_backend_initiPPc+0x20e [0x65e0be]
  [0:3] main+0x36 [0x5e4596]
  [0:4] __libc_start_main+0xf5 [0x2b43821c83d5]
  [0:5] [0x5e76ac]


I have searched the mailing list and the internet but have not found an answer to my satisfaction. I hope someone may have a clue.

Thanks in advance,


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