From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Wed Apr 15 2015 - 09:24:32 CDT
Please try to restart from the recent checkpoint as suggested in the error, and see if it works.
BestPrathit
On Wednesday, 15 April 2015 7:35 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
I have resolved the error now. It requires application of the fix_martini script to run the system.
However, currently I am facing this error now:
FATAL ERROR: Periodic cell has become too small for original patch grid!Possible solutions are to restart from a recent checkpoint,increase margin, or disable useFlexibleCell for liquid simulation.
Even though useFlexibleCell is set to 'no' and my box dimensions cover the entire system. Moreover I have set the center correctly. Can anyone provide more insight please?
On Wed, Apr 15, 2015 at 4:21 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
I keep on getting similar errors like:
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR P5 P5 (ATOMS 1 2)
I have shifted the peptide by 5, 7.5 and 10 angstroms to study the interaction between two molecules. Has anyone else here faced a similar error/situation?
On Wed, Apr 15, 2015 at 4:09 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
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)
RegardsSourav Ray
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