AW: Amber forcefield in namd simulation in parallel version

From: Norman Geist (
Date: Thu Dec 01 2016 - 07:58:00 CST

I’m using _only_ amber files for hundreds of simulation of all kinds. So it works generally without problems, indicating that something is wrong with your prmtop file. How did you obtain that file?


Norman Geist


Von: [] Im Auftrag von Santanu Santra
Gesendet: Donnerstag, 1. Dezember 2016 13:36
Betreff: namd-l: Amber forcefield in namd simulation in parallel version


I would like to ask about using amber 7 prmtop file in namd 2.8 version simulation for a protein , the output file generated , is showing error like that:

Reading parm file (insulin_test.prmtop) ..
PARM file in AMBER 7 format
FATAL ERROR: Failed to read AMBER parm file!
[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x72 [0x4f11a2]
  [0:1] _ZN9NamdState14configListInitEP10ConfigList+0xee4 [0x942cb4]
  [0:2] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x42d [0x9c28fd]
  [0:3] TclInvokeStringCommand+0x88 [0xbc5b98]
  [0:4] [0xbc87b7]
  [0:5] [0xbc9bd2]
  [0:6] Tcl_EvalEx+0x16 [0xbca3f6]
  [0:7] Tcl_FSEvalFileEx+0x151 [0xc2c5a1]
  [0:8] Tcl_EvalFile+0x2e [0xc2c75e]
  [0:9] _ZN9ScriptTcl4loadEPc+0xf [0x9c166f]
  [0:10] main+0x425 [0x4f5995]
  [0:11] __libc_start_main+0xfd [0x36c361ed1d]
  [0:12] [0x4f0a39]
MPI_ABORT was invoked on rank 9 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


When I search it in namd forum, someone specified to delete the scee and scnb section in prmtop file. By doing that also , my work is not running and producing same error.

 Someone specified in namd forum to check whether any path issues are there or not. I have kept all required file in same directory. But still it is not running.

 If anyone can suggest anything ,,, I will be highly grateful.

 Thanks in advance

Santanu Santra

Phd Scholar

Molecular simulation laboratory

Department of chemistry



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