From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Dec 16 2015 - 09:57:47 CST
here is a thought:
The error has nothing to do with what you are trying to do to the system.
It originates because you are not using the correct PDB and/or its
corresponding PSF.
Are you sure that the files that you are reading into NAMD are correct?
Meaning are you sure you give the config file the same name for (PDB/PSF
pair) which you show excerpts above?
On Thu, Dec 17, 2015 at 4:23 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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
>
>
>
>
>
-- Best, /A
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