five 'ERROR' in the log file of NAMD2.9

From: ypg (ypg_at_biophy.nju.edu.cn)
Date: Sun May 13 2012 - 02:15:27 CDT

Dear NAMD experts,

There are five strange ERROR symbol appear in my log file produced by NAMD2.9 just like this:

Info: PARAMETER file: CHARMM format!
Info: PARAMETERS /gpfsTMP/wangwei/ypg/NAMD/ff/par_all27_prot_lipid_CRO2.txt
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES YFP+_eq3.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 194 BONDS
Info: 473 ANGLES
Info: 601 DIHEDRAL
Info: 51 IMPROPER
Info: 6 CROSSTERM
Info: 123 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
ERROR
ERROR
ERROR
ERROR
ERROR
Info: TIME FOR READING PSF FILE: 0.243933
Info: TIME FOR READING PDB FILE: 0.0932858

These ERRORs would not appear if I use NAMD2.7.

It seems that there is something wrong in my force field file, and I indeed have modified my parameter file to define a new type residue. However, these ERRORs would not terminate my simulations and I can still obtain plausible MD results. Also, ERRORs only appear when my system involve the new type residue.

Now I'm really worrying about the validity of my simulated results. I will be highly appreciate for any help!

ypg

 2012-05-13

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