VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Sep 03 2013 - 11:57:54 CDT

Surya,

You will have to provide more information for me to assess this report. Specifically if you could send me psf, pdb, par, and hessian log files (you can zip up and send these to me off-list), I'll take a look.

Regards,
Christopher Mayne

On Sep 3, 2013, at 11:54 AM, surya narayanan chandrasekaran wrote:

hi,

Another error with respect to Bond angle opt. some of the bond and angle parameter FFTK failed to recognise after doing the optimisation the bond and agle values were left 0 in my calculation and i gave it in the guess section and gave the respective .par .pdb .psf then in VMD console window it shows unusual error

.Info) Using plugin namdbin for coordinates from file min-bondangles.coor
Info) Finished with coordinate file min-bondangles.coor.
Info) Opened coordinate file namd-temp.pdb for writing.
Info) Finished with coordinate file namd-temp.pdb.
Info) Opened coordinate file namd-temp.dcd for writing.
Info) Finished with coordinate file namd-temp.dcd.
ERROR) Invalid last frame: 1

 and in the log file its is writing

Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )

thnku
surya

On Tue, Sep 3, 2013 at 4:35 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
All,

Sorry for the delayed response to this issue, as I was out of the country for a bit.

After some testing I have tracked down the problem that was causing this error--the build script was not setting variables containing lists properly. I have fixed and committed the code, which should appear in the next VMD 1.9.2 alpha build. However, in the process of fixing these errors, I have uncovered another issue that will prevent users from executing the bond/angle optimization while VMD is in text mode. The bond/angle optimization utilizes some functions in QMtool that call tk-specific commands, yielding an error when VMD is in text mode. I have added a check to the run script to make sure that tk is available, and a graceful exit where it is not, but this defeats the purpose of the most obvious use cases for the run script. I'm working on better solutions.

Regards,
Christopher Mayne

On Aug 26, 2013, at 10:16 AM, surya narayanan chandrasekaran wrote:

hi,

I was trying to run Bonded_opt with the generated TCL script in that i have 3 .par file but on compiling the script i am getting the following error. It seems to be due to multiple parameter file.
any suggestions with respect to other missing parameter error explanation will be more helpfull.

when i run in GUI the output is running normally.

i also would like to know what are the parameter return in the log file.

Current objective value: 614422.992016 ( En: 614409.213038 Geom: 13.778978 )

  0 1 MG NPH1 Eq: 2.158 Fc: 241.419 GeomDelta: -0.006 EnDelta: 5.844

-- Info) /project/molife/uksoft/lib/vmd/plugins/LINUXAMD64/molfile
1.4
1.3
1.3
1.0
/project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL_MG_charg_HT.psf
/project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL_opt.pdb
/project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/hess_BCL2.log
min-bondangles
namd2
BondedOpt.log
wrong # args: should be "set varName ?newValue?"
wrong # args: should be "set varName ?newValue?"
wrong # args: should be "set varName ?newValue?"
OPTTEMP.par
can't read "::ForceFieldToolKit::BondAngleOpt::namdEnCommand": no such variable
/project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL.par
0.25
0.0
1000.0
10.0
0.0
300.0
0.03
0.1
3.0
5.0
0.001
wrong # args: should be "set varName ?newValue?"
1500
500
500
500
1
0
1.0
1.0
==================================
 Bond/Angle Optimization Settings
==================================

INPUT
psf: /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL_MG_charg_HT.psf
pdb: /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL_opt.pdb
Parameter Files:
        In-Progress PAR File: /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL.par
        All PAR Files (in-progress + associated):
can't read "::ForceFieldToolKit::BondAngleOpt::parlist": no such variable
1
Info) VMD for LINUXAMD64, version 1.9.2a29 (June 12, 2013)
Info) Exiting normally.

this is script par file generated

set ::ForceFieldToolKit::BondAngleOpt::parlist /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL_DFT_bonded.par /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/par_all27_prot_lipid_cmap.inp /project/data/schandrase/Bch1/Gaussian_BCL/NO_TAIL/DFT/CHARGE/Force_field/VMD_1.2a_charge/VMD_1.2a_charge/full_mg/total/BCL.par
set ::ForceFieldToolKit::BondAngleOpt::tempParName OPTTEMP.par

Suryanarayanan C
M.S Chemist 

--
Suryanarayanan C
M.S Chemist
01742857830