VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Tue May 28 2013 - 11:09:20 CDT

This issue might be a result of not having the "geom=PrintInputOrient" command in the route line.
HOwever, without seeing the gaussian log or input file it is only a guess.

brian

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of surya narayanan chandrasekaran [sonofsunsurya_at_gmail.com]
Sent: Monday, May 27, 2013 9:02 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: regarding FFTK

Hi,

I was trying to develop force field for a phorphrin magnesium complex. When i was in the charge optimization step i am having two kinds of problem.

1) some of the water molecule after first step of RHF calculation seems to be bonded on visualization and the number of frames for energy minimization also pretty less compared to other water molecule number of frames. I cross checked the initial file(.gau) for calculation its perfectly fine. anyway Gaussian does not showed it as an error neither the FFTK.

2)I am getting this error during opt.charges step. I am sending you the link of PSF PDB PAR and log files in dropbox kindly have a look at it if you want.

  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 215)
    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)

https://www.dropbox.com/sh/6klo7fzbgshgtnk/LpfqxDz-Pf/forcefield?n=106188702 

--
Suryanarayanan C
M.S Chemist
+94-01794019116