VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Apr 15 2013 - 11:54:54 CDT

Carolina,

The error is being thrown when attempting to measure various distances between your molecule and the optimized position of the water molecule, so it does not appear to be related to the inclusion of the MP single point energy (which is used solely for obtaining the dipole moment).

I am not able to reproduce this error with any of my test files. I'll need access to your files in order to track down specifically what is causing this. Can you post them someplace where I can gain access?

Regards,
Christopher Mayne

On Apr 15, 2013, at 9:40 AM, Carolina Penhavel de souza wrote:

I'm using the fftk in VMD version 1.9.2a19, available in Biocore. In the step "Opt-Charges", I'm having a problem. In the step "Run Optimization", the program send me a error message:

 measure bond: must specify exactly two atoms in a list
 measure bond: must specify exactly two atoms in a list
    while executing
"measure bond "[$temp1 get index] [$temp2 get index]" frame $i"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 152)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)

and, in the vmd console, is written

Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.

In this version of VMD, different of the last version, in the step "Opt-Charges > QM Target Datas" there are two input for the Cpmd log: that is: "Cpmd log (HF)" and "Cpmd log (MP2)". Differently, in the last versions of the VMD there was only "Cpmd log". This error may be related to this?

Thanks,

Carolina.

Carolina Penhavel de Souza
Mestranda em Biofísica Molecular
UNESP - São José do Rio Preto