VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 16 2015 - 10:14:12 CST

You are right. Sorry for having posted
francesco

On Wed, Dec 16, 2015 at 4:57 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
>