From: Santanu Santra (santop420_at_gmail.com)
Date: Thu Dec 01 2016 - 06:36:24 CST
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
NIT ROURKELA
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