From: Santanu Santra (santop420_at_gmail.com)
Date: Thu Dec 01 2016 - 23:00:45 CST
I have created prmtop file in xleap and then minimize my protein in serial
version (CPU) , then it was working, but after that when I started to
rescale in HPC (Parellel version) it is writing few lines in output file
and some error came like that above:
Reading parm file (protein_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.
On Thu, Dec 1, 2016 at 7:28 PM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:
> 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:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Santanu Santra
> *Gesendet:* Donnerstag, 1. Dezember 2016 13:36
> *An:* namd-l_at_ks.uiuc.edu
> *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
>
> NIT ROURKELA
>
>
>
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