VMD-L Mailing List

From: Carolina Penhavel de souza (carolpenhavel_at_hotmail.com)
Date: Wed Oct 03 2012 - 09:19:55 CDT

I installed the version 1.9.2 alpha, but it's not working . When I type
"vmd" on terminal, it seems vmd open, but the "vmd main" and "open
display" windows don't open. Someone knows what is the reason?

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

From: him.upadhyay_at_my.ndsu.edu
To: carolpenhavel_at_hotmail.com
CC: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: question about fftk
Date: Tue, 2 Oct 2012 19:55:30 +0000

Hi Carolina,

log into BioCoRE online. In the menu on the left, select "BioFS Shared Filesystem". Find the folder named "alpha". This folder contains VMD 1.9.2 for mac, linux, solaris, win32cuda and win32nocuda files. Pick up whatever you need.

Him Upadhyay

From: Carolina Penhavel de souza [carolpenhavel_at_hotmail.com]

Sent: Tuesday, October 02, 2012 2:42 PM

To: Him Bandhu Upadhyay

Subject: RE: vmd-l: question about fftk

Hi HIm.

I'm not found the version 1.9.2 alpha from BioCore. Can you send me the link??

Thanks,

Carolina.

Carolina Penhavel de Souza

Mestranda em Biofísica Molecular

UNESP - São José do Rio Preto

From: him.upadhyay_at_my.ndsu.edu

To: carolpenhavel_at_hotmail.com

CC: vmd-l_at_ks.uiuc.edu; ehsanzahedinejad_at_gmail.com

Subject: RE: vmd-l: question about fftk

Date: Tue, 2 Oct 2012 19:16:53 +0000

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> 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 and
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