From: Wang (wybjlu_at_yahoo.cn)
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
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:06 CST