VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Dec 08 2014 - 08:28:13 CST

Zoran,

"Additional Associated Parameter Files" are files that contain any parameters required for your molecule that you are NOT attempting to optimize (i.e., not in the "initialized/in-progress parameter file". If you are parameterizing a molecule completely from scratch, then there are no additional PAR files necessary. If you are attempting to parameterize only the parameters that are not in CGenFF or CHARMM, then you will need to provide the associated file.

The error you are seeing is because you have not provided a NONBONDED (LJ) parameter for your palladium atom.

Regards,
Christopher Mayne


On Dec 8, 2014, at 6:39 AM, zoran wrote:

Dear all,
Recently I‘ve used fftk to parametrize small ligand containing palladium(II) metal. Everything went OK since I have opt-bonded to do. I placed all the items needed that opt-bonded requested. Only one thing I was not sure: In the input section (Additional Associated Parameter Files) do I have to place charmm or any other prm file?
So where is the problem: First in the section Parameters to Optimize when I push Guess button there are no all the bonds and angles. Do I have to manually add missing bonds and angles with corresponding lengths and angles (I can only take them from optimized structure). Here still exists question about force constant values (do I have to write any numbers or what?) since just guessed bonds and angles fftk writes these force constant values. Obviously here is the problem because when I push “Run Optimization” namd failed to further execution and in the log file wrote:
“
..................
............
Info: SUMMARY OF PARAMETERS:
Info: 22 BONDS
Info: 72 ANGLES
Info: 45 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 8 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 27 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG321 NG2R53 PD2 (ATOMS 1 9 17)
child process exited abnormally
    while executing
"::exec D:/NAMD_2.10b2_Win64-multicore/namd2.exe min-bondangles.conf"
    ("eval" body line 1)
    invoked from within
"eval ::exec [list $exec_path] [lrange $args 1 end]"
    (procedure "::ExecTool::exec" line 14)
    invoked from within
"::ExecTool::exec $namdbin $minName.conf"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 68)
    invoked from within
"$function $p0list"
    (procedure "construct_initial_simplex" line 22)
    invoked from within
"construct_initial_simplex [lindex $args 0] $scale"
    (procedure "::Optimize::Opt0::handle" line 91)
    invoked from within
"$opt initsimplex $baInitial $scale"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 322)
    invoked from within
"::ForceFieldToolKit::BondAngleOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
    invoked from within
"::ForceFieldToolKit::gui::baoptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed; .fftk_gui.hlf.nb.bondangleopt...."
    (command bound to event)”

Does any of You have similar problem so he/she can advice me what to do?

cheers
zoran matovic


Dr Zoran D. Matović, professor of chemistry
Head of the Department of Chemistry
Department of Chemistry
Faculty of Science
University of Kragujevac
34000 Kragujevac
Serbia

Tel/Fax + 381 34 336 223 / 381 34 335 040

web-site:
http://www.pmf.kg.ac.rs/~zmatovic/index.htm

Lab for Supercomputing:
http://kraguj.pmf.kg.ac.rs/index.htm
<zoran matovic matović.vcf><pdobp-opt.pdb><log.log>