VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 03 2012 - 13:57:11 CDT

Hi,
  Yes, it appears that you did install the "text" version. You don't
want to use that version, you should delete that one and install the
graphical version ("opengl") instead. I have just posted a fresh
set of VMD builds. You should download and install this one specifically:
  vmd-1.9.2a14.bin.LINUXAMD64.opengl.tar.gz

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 03, 2012 at 01:42:14PM -0300, Carolina Penhavel de souza wrote:
> Hi John!
>
> Really, I download and installed the "text" version. I type "vmd" on
> terminal e, after, I run the command "vmdinfo options" and it send me
>
> "LINUXAMD64 ACTC IMD LIBTACHYON NETCDF TCL PTHREADS SILENT".
> Do you know why the "main VMD" and "Display graphics" windows aren't
> opening?
>
> Thank you,
>
> Carolina.
>
> Carolina Penhavel de Souza
> Mestranda em Biofisica Molecular
> UNESP - Sao Jose do Rio Preto
>
> > Date: Wed, 3 Oct 2012 11:20:40 -0500
> > From: johns_at_ks.uiuc.edu
> > To: carolpenhavel_at_hotmail.com
> > CC: him.upadhyay_at_my.ndsu.edu; vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: question about fftk
> >
> >
> > Hi,
> > Did you install the "text" version? I posted a special "text-only"
> version
> > of VMD for one of the other VMD users that requested it. If you grabbed
> > that version, that will explain your problem. Try running this command
> inside
> > the VMD that you installed:
> > vmdinfo options
> >
> > And let me know what it says.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Oct 03, 2012 at 11:19:55AM -0300, Carolina Penhavel de souza
> wrote:
> > > 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 Biofisica Molecular
> > > UNESP - Sao Jose 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 Biofisica Molecular
> > > UNESP - Sao Jose 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 Biofisica Molecular
> > > UNESP - Sao Jose do Rio Preto
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078