VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Mon Aug 26 2013 - 10:16:02 CDT

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