not fatal error but no more information

From: Wang (
Date: Thu Apr 04 2013 - 13:50:17 CDT

Hi Guys, I got this kind of error in the output file and there are no more information. Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED     1347475938 Info: USE HYDROGEN BONDS?    NO Info: COORDINATE PDB         ../step5_assembly.pdb Info: STRUCTURE FILE         ../step5_assembly.xplor_ext.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS             toppar/par_all22_prot.prm Info: PARAMETERS             toppar/par_all27_na.prm Info: PARAMETERS             toppar/par_all36_carb.prm Info: PARAMETERS             toppar/par_all36_lipid.prm Info: PARAMETERS             toppar/par_all36_cgenff.prm Info: PARAMETERS             toppar/myco.prm Info: PARAMETERS             toppar/heme.prm Info: PARAMETERS             toppar/toppar_water_ions.str Info: PARAMETERS             toppar/toppar_all36_lipid_cholesterol.str Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES     step6.1_equilibration.coor Info: FIRST TIMESTEP         35000 Info: SUMMARY OF PARAMETERS: Info: 878 BONDS Info: 2516 ANGLES Info: 5813 DIHEDRAL Info: 179 IMPROPER Info: 6 CROSSTERM Info: 340 VDW Info: 6 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Warning: Ignored 13206 bonds with zero force constants. Warning: Will get H-H distance in rigid H2O from H-O-H angle. ERROR ERROR ERROR ERROR ERROR ERROR  ERROR Info: TIME FOR READING PSF FILE: 5.57084 Info: READING EXTRA BONDS FILE restraints/step6.2_equilibration.dihe Info: READ 156 EXTRA IMPROPERS Info: TIME FOR READING PDB FILE: 0.128875 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 67051 ATOMS Info: 53682 BONDS Info: 65190 ANGLES Info: 73455 DIHEDRALS Info: 1594 IMPROPERS Info: 432 CROSSTERMS Info: 0 EXCLUSIONS Info: 55135 RIGID BONDS Info: 146018 DEGREES OF FREEDOM Info: 25122 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 25122 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 410982 amu Info: TOTAL CHARGE = 1.41039e-05 e Info: MASS DENSITY = 0.944522 g/cm^3 Info: ATOM DENSITY = 0.0927973 atoms/A^3 Info: ***************************** Info: Reading from binary file step6.1_equilibration.coor This is only the error part. It can still run the MD simulation after the ERROR part. Is anyone know the reason? Thanks, Yibo ----------------- Wang Yibo State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University

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