From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Thu Apr 16 2015 - 11:37:21 CDT
I don't have a clear idea regarding this, but I think the distance between the two peptides may have a role to play in this.
Please try restraining the peptides and equilibrating the solvent for sometime, and slowly release the restraint. If that does not work, please see whether keeping the peptides at a greater distance resolves the problem.
Also, please check the box dimensions, how far are they deviating w.r.t. their original values?
If the above two solutions don't work, please re-shoot a mail to the namd experts. Regards,Prathit
On Thursday, 16 April 2015 5:04 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
I think the problem is box distortion, there was no such issue while doing the simulation with a single peptide. I can start from recent checkpoint but ultimately it's not a permanent fix as I have to keep on doing it.
On Wed, Apr 15, 2015 at 7:54 PM, Prathit Chatterjee <pc20apr_at_yahoo.co.in> wrote:
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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