From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Aug 25 2015 - 19:30:52 CDT

Eddie,

You're using one of the alpha versions of 1.9.2 build in May. The final release of 1.9.2 was built in Dec (2014). Diffing your qmtool_readwrite.tcl against 1.9.2 final release indeed shows changes to the parser that I put in before the final release version. So, try installing the official 1.9.2 release and that should fix the errors you're getting.

Regards,
Christopher Mayne

On Aug 25, 2015, at 10:41 AM, Prof. Eddie wrote:

Hi Christopher,
No errors occur when IImport the Optimized geometry. I get the error when I load the hessian file (import hessian/charges from a single point calculation).
I am running: Info) VMD for LINUXAMD64, version 1.9.2a26 (May 9, 2013)

I had to modify QMtool::read_gaussian_espcharges to get the charges, but I don't understand this error.

Here is some of the output:
Info) Using plugin pdb for structure file /home/eddie/code/namd/output/param/lc_geo_hess_qmtool_tmp.pdb
Autopsf: Updating structures
Info) Using plugin pdb for coordinates from file /home/eddie/code/namd/output/param/lc_geo_hess_qmtool_tmp.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file /home/eddie/code/namd/output/param/lc_geo_hess_qmtool_tmp.pdb.
Info) Analyzing structure ...
Info) Atoms: 38
Info) Bonds: 39
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
0: SCF = -747.157052 hart = -468534.906814 kcal/mol; rel = 0.0000 kcal/mol
 Temperature 298.150 Kelvin. Pressure 1.00000 Atm.

****************************************************************
********************* Thermochemistry **********************
********************* **********************
****************************************************************

Gas phase:
================================================================
Eletronic energy E(vacuum) = -470394.38 Kcal/mol
Zero-point energy ZPE = 203.86 Kcal/mol
Internal energy U(298.150K) = 215.28 Kcal/mol
Enthalpy H(298.150K) = 215.88 Kcal/mol
Entropic term T*S = 42.58 Kcal/mol
Gibbs free energy G(298.150K) = 173.30 Kcal/mol
E(vacuum) + ZPE = -470190.52 Kcal/mol
E(vacuum) + U(298.150K) = -470179.10 Kcal/mol
E(vacuum) + H(298.150K) = -470178.51 Kcal/mol
E(vacuum) + G(298.150K) = -470221.09 Kcal/mol
Entropy S = 0.14 Kcal/(mol*K)
Heat capacity CV = 68.75 Cal/(mol*K)

****************************************************************
****************************************************************

internal hessian size = 201

Maybe you diff my tcl files with yours?
Thanks,
Eddie

On Tue, Aug 25, 2015 at 9:48 AM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Eddie,

I'm not able to reproduce your error. From the supplied hessian LOG file I was able to use both QMTool and Paratool to load in the Hessian data both to obtain charges as well as to visualize Hessian terms.

1) Make sure that you are using VMD 1.9.2 (or higher). In the not too distant past I had to modify the file parsers due to some changes in keywords from the Gaussian LOG files.
2) Can you tell me *exactly* what steps you are doing to get this error?

Regards,
Christopher Mayne

On Aug 25, 2015, at 8:48 AM, Prof. Eddie wrote:

Hi Christopher,
The g09 runs are successful (geom opt is lc_geo_opt.log and the hess is lc_geo_hess.log). I get an error of
can't use empty string as operand of "*"
can't use empty string as operand of "*"
    while executing
"expr {3*$natoms}"
    (procedure "load_gaussian_log" line 50)
    invoked from within
"load_gaussian_log $file"
    (procedure "::QMtool::load_file" line 10)
    invoked from within
"::QMtool::load_file $file [string range [file extension $file] 1 end]"
    (procedure "load_molecule" line 14)
    invoked from within
"load_molecule SIP $file"
    (procedure "::Paratool::opendialog" line 131)
    invoked from within
"::Paratool::opendialog loadsip "[file rootname ${::Paratool::molnamebase}]_sp""
    invoked from within
".paratool.#paratool#menu.#paratool#menu#hessian invoke active"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke active]"
    (procedure "tk::MenuInvoke" line 50)
    invoked from within
"tk::MenuInvoke .paratool.#paratool#menu.#paratool#menu#hessian 1"
    (command bound to event)

Thanks,
Eddie

On Tue, Aug 18, 2015 at 3:58 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
We have very much deprecated Paratool in favor of ffTK; however, we've tried to keep QMTool as functional as possible. It appears that the error is occurring in the QMTool parser. If you send your PSF, PDB and Gaussian IO files I'll take a look to try and figure out where the parser is choking.

Regards,

Christopher Mayne

On Aug 18, 2015, at 1:09 PM, Prof. Eddie wrote:

Hi,
I am using paratool for a first pass before fftk (in the end I want to build a course grain model so my parameter's need not be perfect). I fixed the problem with g09 and now it does converge, but I still get the same error parsing the file.

I can modify the qm_tool.tcl files to fix the problem (at least this problem, then another comes up). Is paratool really completely deprecated and can't parse g09 files anymore? Or are there patches somewhere I can use?
Thanks,
Eddie

On Mon, Aug 17, 2015 at 11:09 PM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
Hi,
  Paratool has been (greatly) superceded by ffTK in recent versions of VMD,
so if you're developing parameters I would suggest using ffTK instead.
If you're doing something else (e.g. only using qmtool and not paratool)
maybe you could provide more commentary on this and someone might be able
to make a helpful suggestion. My assumption from the errors you provided
below is that there are issues with parsing the output from g09 which
terminates subsequent processing after that point.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Mon, Aug 17, 2015 at 02:52:20PM -0500, Prof. Eddie wrote:
> Hello,
> I'm trying to import the charges calculated via the Hessian (from paratools
> Qm gui). I keep getting the error:
> invalid bareword "Sum"
> in expression "Sum-1";
> should be "$Sum" or "{Sum}" or "Sum(...)" or ...
> invalid bareword "Sum"
> in expression "Sum-1";
> should be "$Sum" or "{Sum}" or "Sum(...)" or ...
> (parsing expression "Sum-1")
> invoked from within
> "expr [lindex $line 0]-1"
> (procedure "read_gaussian_espcharges" line 30)
> invoked from within
> "read_gaussian_espcharges $fid"
> (procedure "read_gaussian_log" line 360)
> invoked from within
> "read_gaussian_log $file $molid"
> (procedure "load_gaussian_log" line 17)
> invoked from within
> "load_gaussian_log $file"
> (procedure "::QMtool::load_file" line 10)
> invoked from within
> "::QMtool::load_file $file [string range [file extension $file] 1 end]"
> (procedure "load_molecule" line 14)
> invoked from within
> "load_molecule SIP $file"
> (procedure "::Paratool::opendialog" line 131)
> invoked from within
> "::Paratool::opendialog loadsip "[file rootname
> ${::Paratool::molnamebase}]_sp""
> invoked from within
> ".paratool.#paratool#menu.#paratool#menu#hessian invoke active"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke active]"
> (procedure "tk::MenuInvoke" line 50)
> invoked from within
> "tk::MenuInvoke .paratool.#paratool#menu.#paratool#menu#hessian 1"
> (command bound to event)
>
>
> I know my convergence is not great since gaussian (09) gives:
> Item Value Threshold Converged?
> Maximum Force 0.000032 0.000450 YES
> RMS Force 0.000004 0.000300 YES
> Maximum Displacement 0.005351 0.001800 NO
> RMS Displacement 0.001625 0.001200 NO
> Predicted change in Energy=-3.071138D-08
>
> but I'm trying to make it better. In the meantime I would at least like to
> know how to fix the problem paratool is having parsing the file. I am using
> vmd 1.9.2 with gaussian09. Any ideas?
> Thanks
> Eddie
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad1wcTmowhlg1zyS7w&e=>>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390<tel:%28618%29%20650-2390>

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Edward Ackad, Ph.D<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.siue.edu_-257Eeackad&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=YHseimfr7S9m8AblVTEdcPdZqYb7fiEgW-3LcL4V0dE&s=fUU2XU0wdKqXoqPw6E_9eo8iVa41wcTmowhlg1zyS7w&e=>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390<tel:%28618%29%20650-2390>
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_________________________________________________________
Edward Ackad, Ph.D<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.siue.edu_-257Eeackad&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=ajzxDxty_4lJmvyZJw0t5YaqQVE3bPIDXazV1lncork&s=LoNWwxzLMMo8Ys-HvBPNmDsLa3PGSbEjCtyIYap9ECE&e=>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390<tel:%28618%29%20650-2390>
<files.tar.gz>
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_________________________________________________________
Edward Ackad, Ph.D<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.siue.edu_-257Eeackad&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=wpQSDpd5yyfHbT_VkUfXcldf7eECRgTmIKvc3gzjSH8&s=9P84N17t0zonVnXMyaRM4mJesUO5D3hxfsi87J5CYBs&e=>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
<qmtool_charges.tcl><qmtool_readwrite.tcl>