VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Mon Jul 22 2013 - 11:08:37 CDT

HI

when doing Dihedral optimization procedure the last tab (opt torison). I
have loaded the respective files and got these following error

FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR NPH1 CPAN CPM2 CPA3
(ATOMS 2 6 7 8)
[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x72 [0x5699a2]
  [0:1]
_ZN10Parameters21assign_improper_indexEPcS0_S0_S0_P8improperi+0x276
[0xa2a566]
  [0:2] _ZN8Molecule13read_psf_fileEPcP10Parameters+0xff2 [0x9d8c92]
  [0:3] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x15d
[0x9d70ad]
  [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x6d6 [0xa05466]
  [0:5] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x5ba [0xa8cfba]
  [0:6] TclInvokeStringCommand+0x73 [0x7f2cc5590ac3]
  [0:7] +0x5b4aa [0x7f2cc55434aa]
  [0:8] +0x5c97c [0x7f2cc554497c]
  [0:9] Tcl_EvalEx+0x16 [0x7f2cc5591a16]
  [0:10] Tcl_FSEvalFileEx+0x100 [0x7f2cc55b19e0]
  [0:11] Tcl_EvalFile+0x24 [0x7f2cc552b4b7]
  [0:12] _ZN9ScriptTcl4loadEPc+0x10 [0xa8ab80]
  [0:13] main+0x449 [0x56dfc9]
  [0:14] __libc_start_main+0xe6 [0x7f2cc40eec36]
  [0:15] [0x52c9e9]
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR NPH1 CPAN CPM2
CPA3 (ATOMS 2 6 7 8)

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
    while executing
"::exec /project/molife/uksoft/Linux-x86_64-MPI/namd2 min-geom.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 $name.conf "
    (procedure "calcMM" line 102)
    invoked from within
"calcMM $psf $pdb $dihToFit $namdbin $parlist"
    (procedure "::ForceFieldToolKit::DihOpt::optimize" line 107)
    invoked from within
"::ForceFieldToolKit::DihOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::doptRunOpt" line 64)
    invoked from within
"::ForceFieldToolKit::gui::doptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.dihopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.dihopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.dihopt.runOpt state !pressed;
.fftk_gui.hlf.nb.dihopt.runOpt invoke } "
    (command bound to event)
*
*
*when i checked my par file the improper angle section is empty *
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5

I found the section empty in tutorial also. I was not able to find the
optimization of it in previous steps. So kindly state me how it is
parametrized? is it need to be done using CHARMM

The second doubt is regarding how the figure 4,6.7 and 8 is generated as
reported in the JCP paper. IS it using FFTK or using the script provided in
Supporting information.

third doubt is about how one can obtain vibrational frequencies as reported
in table 4 because when i looked in the log file for bonded_opt.log only
the force constant is written.

Fourth doubt is regarding Interaction energy. i have some cases like below
where the difference between HF(QME) and Cgenff(MME) is huge but the
optimization says its converged then how much is the data reliable.

C4D QME: -1.371 MME: 8.915 (10.287) QMD: 3.194 MMDistDelta: 0.400
CAD QME: -0.721 MME: 7.686 (8.407) QMD: 3.247 MMDistDelta: 0.400
CGA QME: -2.314 MME: -0.213 (2.100) QMD: 3.682 MMDistDelta: 0.400 

-- 
Suryanarayanan C
M.S Chemist
01742857830