From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 16 2015 - 09:23:41 CST
Hello:
On trying unrestrained minimization (NAMD-multicore 2.11b1) of a psf/pdb
system prepared under charmm36 with VMD (1.9.2) in text mode, I got the
error
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 160 BONDS
Info: 422 ANGLES
Info: 761 DIHEDRAL
Info: 44 IMPROPER
Info: 6 CROSSTERM
Info: 80 VDW
Info: 2 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Found 24 H-H bonds.
Info: TIME FOR READING PSF FILE: 0.121484
FATAL ERROR: Number of pdb and psf atoms are not the same!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR:Number of pdb and psf atoms are not the same!
Actually, as far as I can see from the pdb and psf files, the numbers are
the same:
PDB
ATOM 32174 CLA CLA I 53 -65.452 -7.286 16.803 1.00 0.00 ION
CL
ATOM 32175 CLA CLA I 54 -7.791 -38.624 13.906 1.00 0.00 ION
CL
ATOM 32176 CLA CLA I 55 -15.528 -25.018 -11.043 1.00 0.00 ION
CL
ATOM 32177 CLA CLA I 56 -35.145 -36.098 -9.424 1.00 0.00 ION
CL
ATOM 32178 CLA CLA I 57 -27.805 -13.888 -26.606 1.00 0.00 ION
CL
END
PSF 32172 ION 51 CLA CLA CLA -1.000000 35.4500 0
32173 ION 52 CLA CLA CLA -1.000000 35.4500 0
32174 ION 53 CLA CLA CLA -1.000000 35.4500 0
32175 ION 54 CLA CLA CLA -1.000000 35.4500 0
32176 ION 55 CLA CLA CLA -1.000000 35.4500 0
32177 ION 56 CLA CLA CLA -1.000000 35.4500 0
32178 ION 57 CLA CLA CLA -1.000000 35.4500 0
22132 !NBOND: bonds
1 5 2 1 3 1 4 1
I can only add (besides noticing the above warning in the minimization log)
that, without previous experience as to that, I used two different models
for the molecule of water coordinating the active center (resid 400)and
solvation water (resid 1...) Parameters were furnished to minimization for
both water models
2056 WL 400 TP3M OH2 OT -0.834000 15.9994 0
2057 WL 400 TP3M H1 HT 0.417000 1.0080 0
2058 WL 400 TP3M H2 HT 0.417000 1.0080 0
2059 WT1 1 TIP3 OH2 OT -0.834000 15.9994 0
2060 WT1 1 TIP3 H1 HT 0.417000 1.0080 0
2061 WT1 1 TIP3 H2 HT 0.417000 1.0080 0
however, no warning in the log files about that.
thanks for advice
francesco pietra
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