From: Sourav Ray (souravray90_at_gmail.com)
Date: Wed Apr 15 2015 - 05:39:18 CDT
Hello
Although I have been able to run single molecule coarse-grained simulation.
I faced the following error while running two peptide equilibriation
simulation.
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
[0] Stack Traceback:
[0:0] CmiAbort+0x5f [0xe8725f]
[0:1] _Z8NAMD_diePKc+0x62 [0x663b9a]
[0:2] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0x1de [0xc0d810]
[0:3] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x190 [0xbb3e6e]
[0:4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x3e5 [0xbb117d]
[0:5] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
[0:6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
[0:7] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
[0:8] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
[0:9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
[0:10] TclInvokeStringCommand+0x88 [0xecef58]
[0:11] [0xed1a70]
[0:12] [0xf14853]
[0:13] [0xf1a613]
[0:14] TclEvalObjEx+0x86 [0xed36c6]
[0:15] [0xedc61d]
[0:16] [0xed1a70]
[0:17] [0xed2e56]
[0:18] Tcl_EvalEx+0x16 [0xed3636]
[0:19] Tcl_FSEvalFileEx+0x151 [0xf35441]
[0:20] Tcl_EvalFile+0x2e [0xf355fe]
[0:21] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
[0:22] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
[0:23] main+0x3a [0x6684c2]
[0:24] __libc_start_main+0xf5 [0x7f9c1c22bec5]
[0:25] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
[0] Stack Traceback:
[0:0] [0xe88055]
[0:1] CmiAbort+0x9d [0xe8729d]
[0:2] _Z8NAMD_diePKc+0x62 [0x663b9a]
[0:3] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0x1de [0xc0d810]
[0:4] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x190 [0xbb3e6e]
[0:5] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x3e5 [0xbb117d]
[0:6] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
[0:7] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
[0:8] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
[0:9] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
[0:10] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
[0:11] TclInvokeStringCommand+0x88 [0xecef58]
[0:12] [0xed1a70]
[0:13] [0xf14853]
[0:14] [0xf1a613]
[0:15] TclEvalObjEx+0x86 [0xed36c6]
[0:16] [0xedc61d]
[0:17] [0xed1a70]
[0:18] [0xed2e56]
[0:19] Tcl_EvalEx+0x16 [0xed3636]
[0:20] Tcl_FSEvalFileEx+0x151 [0xf35441]
[0:21] Tcl_EvalFile+0x2e [0xf355fe]
[0:22] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
[0:23] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
[0:24] main+0x3a [0x6684c2]
[0:25] __libc_start_main+0xf5 [0x7f9c1c22bec5]
[0:26] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
Aborted (core dumped)
Regards
Sourav Ray
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