VMD-L Mailing List

From: Him Bandhu Upadhyay (him.upadhyay_at_my.ndsu.edu)
Date: Tue Oct 02 2012 - 14:16:53 CDT

Hi Carolina,
I also had the same problem. I think the problem is when you are generating water interaction gaussian input files, VMD only creates acceptor and donor input files but do not create *-sp.gau file for molecule and water. If this is the case then you are using a old version of ffTK. I suggest that you grab a copy of the latest 1.9.2.alpha builds from BioCoRE.

I hope this helps you

________________________________
Him Upadhyay

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of ehsan zahedinejad [ehsanzahedinejad_at_gmail.com]
Sent: Tuesday, October 02, 2012 11:05 AM
To: Carolina Penhavel de souza
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: question about fftk

Hi Carolina,

When you generate Gaussian input files in "Water Int." of fftk, In addition to those files for Donor-Accepter files it also
generate two input files named "wat-sp.gau" and "your molecule-sp.gau". You should run these two files by Gaussian
and use their output log files in Opt.Charge section.

I hope this helps.
Ehsan.

On Tue, Oct 2, 2012 at 6:26 AM, Carolina Penhavel de souza <carolpenhavel_at_hotmail.com<mailto:carolpenhavel_at_hotmail.com>> wrote:
Hi.

I'm modeling an molecule in fftk and I don't have the files water-sp.log and molecule-sp.log, required in the "Opt.Charges > Input/Settings > QM Target Data" step. I try to generate this files in the Paratool, where I get the files water_sp.com<http://water_sp.com> and molecule-sp.com<http://molecule-sp.com>, and after I run this files on gaussian. However, when I insert this files in fftk, I get this error:

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 154)
    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)

On the tkConsole, the last lines are:

.
.
.
10: SCF = -570.039963 hart = -357466.505972 kcal/mol; rel = -1.2951 kcal/mol
11: SCF = -570.039963 hart = -357466.506028 kcal/mol; rel = -1.2951 kcal/mol
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.
Optimization completed. -- Stationary point found.
Optimization completed. -- Stationary point found.
No mulliken charges found.

How can I to proceed? This problem can be the _sp.log file? If so, how can I to obtain this files?

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