jensengroup / molcalc Goto Github PK

Chrome on linux has some jmol problems (unable to get atom coordinates for calculation)

xhr.open async=true url=https://cactus.nci.nih.gov/chemical/structure/(3z, 5s)-6-ethyl-4-isopropyl-5-methyloct-3-enal/smiles

cactus.nci.nih.gov/chemical/structure/(3z,%205s)-6-ethyl-4-isopropyl-5-methyloct-3-enal/smiles

Failed to load resource: the server responded with a status of 500 (INTERNAL SERVER ERROR)

When computing properties for C(=N)O the energy of heat of formation is different if the structure is drawn vs. feeding the SMILES code. Is it a bug, or does MolCalc apply different settings depending on how the compound is specified?

Hello, I am a teacher and use MolCalc.org regularly during classes to explain molecular orbital theory. First let me thank you for creating such an practical, well-designed, and effective tool. I greatly appreciate the effort that has gone into this. However, Some enhancements would considerably improve the learning experience.

My requests are the following:

1. Serial-number the molecular orbitals since it would greatly help in identifying HOMO and LUMO of the ground state.
2. Show occupancy of electrons (according to Aufbau principle) for the ground state of the molecule.
3. Degenerate molecular orbitals (with the same energy) should be kept side by side.

I have shown an example of how it should look like for the molecular orbitals of a dioxygen molecule:

Thank you for your consideration.

The underlying PM3 method does not support He.

I suppose removing it from the builder would be most obvious solution.

If you delete the molecule you are editing it is still possible to continue to the calculation page which then fails (obviously) because there is no molecule.

I am following the README, yet can not run the calculations. The health check tells that everything is alright. However, Molecule List and About are not found. Pressing the "Calculate Properties" button gets stuck at "preparing molecule for property calculation...". There is something missing that I do not see in the README. Could you please point to that?

For instance, the "GAMESS Note" in the README is not clear. At least for a new user of both molcalc and GAMESS. Should the "data" (tmpfolder) be the same as "SCR" in rungms?

Ubuntu 17.10, PHP5 / Apache2, GAMESS 2018. All fresh and working.

The new beta version struggles to calculate the properties of simple diatomic molecules such as Li2, C2, and N2.

The Li2 calculation fails to compile because it can't determine the solvation properties.
The N2 calculation does not compile unless Molcalc adds hydrogens and processes it as N2H4.
The C2 calculation does not compile unless Molcalc adds hydrogens and processes it as C2H4.

Hi everyone, is there a way to see the contribution of the various atomic orbitals to the molecular ones, also to have the OM diagram?

I wanted to bring to your attention an issue I encountered using the website Specifically, I'm having difficulty navigating to the "Help" and "About" pages within the application.

Upon attempting to access these pages , site keeps on loading . As a result, I'm unable to access important information and resources that may be available in these sections.

Could you please verify whether this issue is valid and whether others have reported similar problems? If it is indeed a bug or a usability issue, I would like to offer my assistance in addressing it.

@charnley @vladislavivanistsev

I was trying to use your amazing software to calculate a dipole moment for 2,2-bis(trifluoromethyl)-1,1-dicyanoethylene. The system blocked me due to the molecule having greater than 10 heavy atoms. I'm wondering if there is any way around this? I would be willing to pay. Perhaps have a paid version of the software that allowed for a greater tax on the servers would be useful to other users as well.

Atomic orbital calculations for single atoms with an even number of electrons do not compile for atoms such as Mg like they do in the old version.

When the orbital calculations do compile, they default to a molecule that wasn't queried. For example, in the case of a C atom, the atomic orbital calculation defaults to a calculation for CH4 molecular orbitals.

Error when trying to do calculations on http://molview.org/?cid=22385494 (NH3+CHO) and http://molview.org/?cid=19073436 (NHCHO-)

Warning: file_get_contents(http://cactus.nci.nih.gov/chemical/structure/C(%3DO)%5BNH3%5D/iupac_name) [function.file-get-contents]: failed to open stream: HTTP request failed! HTTP/1.1 404 NOT FOUND in /srv/www/molcalc/methods/initialize/initialize.php on line 53
71dcd0472db547597459b8ed463325bb

Would you be able to add the atomic and ionic radius of the atoms/ions? Thanks

Hi @charnley and @vladislavivanistsev!

I'm a chemistry student from Toronto, Canada, and am a huge fan of this tool - MolCalc! I think it is clean, easy-to-use and it has definitely taught me a lot about molecules. I don't have an actual issue for you to fix, but instead two questions to further my knowledge:

1. what type of surface area is being calculated in the value "Surface Area"? Is it van der Waals surface area, or solvent accessible surface area?
2. How is "Total Solvation Energy" being calculated?

Thanks for developing this awesome visualizer, and let me know!
Ashna

Hi,

the screenshot includes the mispelled word "minimise". Perhaps that screenshot should be updated in the manual and also in a possible future correction of the manuscript.

cheers

I noticed that the About page on molcalc.org states "Yes, MolCalc is distributed through GitHub under the GPL license," but there is no license in the repo. I saw a LICENSE file in the MolCalc-1.3 repo, though there does not appear to be a full GPL license there either.

If the project is intended to be distributed under a version of GPL, would it be possible to have a proper GPL license file added? That way, I can ensure that I'm using and extending MolCalc under the proper license.

Thanks!

Is it possible to define a bond length (or angle) before submitting calculation? For example, could you calculate the thermodynamic properties of H2 with a bond length of 0.100 nm?

To draw two molecules one has to "extend" a pre-existent one and then delete the bridge atom. Could it be possible to draw directly the extra molecule?

In the listing of orbital energies, what defines the zero reference point of these numbers? It would be nice to have an explanation right on the site. I tried to ask the community about this (https://chemistry.stackexchange.com/questions/128544/for-molecular-orbitals-how-is-an-energy-of-zero-set-or-defined), but I did not receive an answer that is "student-ready". It is very difficult to find MO-diagrams with an energy axis, eventhough the order of orbitals is discussed extensively in textbooks.

Would it be possible to include the ability to change the spin multiplicity of the molecule? I see questions come up on reddit.com/r/askchemistry about singlet vs triplet orbitals, geometries, etc.

By June 19, 2015 Jan Jensen commented on chemistry.stackexchange

Don't know if this help but you can compute the canonical MOs (at the RHF/STO-3G//PM3 level of theory) using molcalc.org

The web site offers benzene as an example of an organic (aromatic) molecule to get familiar with the program, e.g. the computation and subsequent display of molecular orbitals one can select one by one

of which HOMO, and LUMO can be of particular interest.

I would like to suggest a modification the display of the MO's. In addition to the current table, please add

• an explicit label (HOMO, SOMO, or LUMO) next to the orbital's energy in the tabular representation
• there already is a toggle to change the molecule's representation either as ball-and-strick, or wire model. Please extend the present interface, and add a button to access either HOMO, or LUMO directly with a single click. Then, there no longer is a need to browse through the table to manually pick these peculiar MOs in question. An explicit indicator e.g., the top right corner of JSmol's display with a report like MO 03/20 to indicate it is the third MO of twenty were welcome. (Then, the documentation of molcalc should describe if the sort starts by low energies, or high energies.) Equally – and independent of the former suggest – let there be an explicit indicator e.g., the top right corner of JSmol's display if – if this indeed is the case – the MO displayed is HOMO, SOMO, LUMO – independent of the suggested display MO 03/20.

Using the searchbar to find 'carbon monoxide' results to 'formaldehyde'. It seems the software forces adding hydrogens.

The error message is as follows: "Error. Server was unable to run solvation calculation" with both iodoalkanes and fluoroalkanes.

Triple bonds look hideous. In order for them to look better I set the following variables:

set bondRadiusMilliAngstroms 100
set multipleBondSpacing -0.3

Check the following link for an explanation of the spacing sign
http://www.mail-archive.com/[email protected]/msg15694.html

These settings look fine also for double and single bonds.

Occurs on not all, but many molecules. Error is as follows:

Warning: file_get_contents(http://cactus.nci.nih.gov/chemical/structure/%5BLi%5Dc1cc(F)c(F)c(F)c1/iupac_name) [function.file-get-contents]: failed to open stream: HTTP request failed! HTTP/1.1 404 NOT FOUND in /srv/www/molcalc/methods/initialize/initialize.php on line 53
7b4558bddc63c9a67a1e0c06fc2f6b51

It would be nice to have an Orbital Diagram filled out as an output as well. Thanks

When I try to look for an molecule such as HCl, it says that I don't have internet connection and says to me to wait and try again. However, I have internet connection. Can you please fix this issue, I need to use the website very urgently.

The grey atoms of the structure can sometimes have larger radii than parts of the core electron orbitals themselves. Some kind of option to change to transparent or stick structure would be appreciated, thanks!

For example if I want to calculate the orbital energy of H atom, which is -13.6eV for n=1
Or O atom etc

$ ls data/
3ccab5ef041634fc1b7db4ad897e96b5 61147a6682500baa0150a29b9b1b340b
4cbc93d6590db82284385d1d7ac8b805 ba9091c120118ad126ef24fc87bfc354

$ ls data/61147a6682500baa0150a29b9b1b340b/
61147a6682500baa0150a29b9b1b340b.dat coordinates_jmol.xyz molecule.db
61147a6682500baa0150a29b9b1b340b.inp coordinates.mol2 thumbnail.png
61147a6682500baa0150a29b9b1b340b.log coordinates.xyz

$ tail ~/sf_install/apache/logs/error_log
cp 3ccab5ef041634fc1b7db4ad897e96b5.inp /home/dokuwiki/www/molcalc/data/3ccab5ef041634fc1b7db4ad897e96b5/3ccab5ef041634fc1b7db4ad897e96b5.F05
unset echo
/home/dokuwiki/sf_box/gamess/ddikick.x /home/dokuwiki/sf_box/gamess/gamess.00.x 3ccab5ef041634fc1b7db4ad897e96b5 -ddi 1 1 dokuwiki -scr /home/dokuwiki/www/molcalc/data/3ccab5ef041634fc1b7db4ad897e96b5
unset echo
ls: No match.
ls: No match.
ls: No match.
1 molecule converted
16 audit log messages
1 molecule converted
20 audit log messages
1 molecule converted
27 audit log messages
1 molecule converted
15 audit log messages
1 molecule converted
15 audit log messages
[Thu Jun 08 23:31:42.978000 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: get_headers(): SSL operation failed with code 1. OpenSSL Error messages:\nerror:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 20, referer: http://172.16.11.179:8008/molcalc/
[Thu Jun 08 23:31:42.978155 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: get_headers(): Failed to enable crypto in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 20, referer: http://172.16.11.179:8008/molcalc/
[Thu Jun 08 23:31:42.978307 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: get_headers(http://cactus.nci.nih.gov/chemical/structure/C%5BSiH3%5D/iupac_name): failed to open stream: operation failed in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 20, referer: http://172.16.11.179:8008/molcalc/
[Thu Jun 08 23:31:44.744321 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: file_get_contents(): SSL operation failed with code 1. OpenSSL Error messages:\nerror:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 53, referer: http://172.16.11.179:8008/molcalc/
[Thu Jun 08 23:31:44.744355 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: file_get_contents(): Failed to enable crypto in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 53, referer: http://172.16.11.179:8008/molcalc/
[Thu Jun 08 23:31:44.744391 2017] [:error] [pid 8786:tid 140065820882688] [client 172.16.3.21:54227] PHP Warning: file_get_contents(http://cactus.nci.nih.gov/chemical/structure/C%5BSiH3%5D/iupac_name): failed to open stream: operation failed in /home/dokuwiki/www/molcalc/methods/initialize/initialize.php on line 53, referer: http://172.16.11.179:8008/molcalc/
1 molecule converted
46 audit log messages
[Thu Jun 08 23:31:44.930610 2017] [:error] [pid 8786:tid 140065810392832] [client 172.16.3.21:54227] PHP Parse error: syntax error, unexpected 'else' (T_ELSE) in /home/dokuwiki/www/molcalc/views/pages/calculation.php on line 119, referer: http://172.16.11.179:8008/molcalc/

How should I install the ppqm package?

Hello, I wrote yesterday that the website wasn't working and you fixed it. I think it is broken again can fix it? Thank you.

See the following example for 2-fluoropropane.

Submitting multi-molecules via the interface is breaking

• number of atoms check
• get_name check
• probably other things

Should add manual multi-smiles check to workflow

Whenever I try to obtain data for pyridine, I get a "too many steps" error.

The views.py file contains several views and helper functions related to handling user requests, rendering templates, and performing calculations. However, the code could benefit from some optimization and refactoring to improve its readability, efficiency, and maintainability.

(e)-but-2-ene is correctly named, but the 2D representation shows (z)-but-2-ene.

The new version gives a surface area of 156 A^2 for NH4+, while the legacy version gives 42 Å^2. The latter is correct

Creating a printout feature, thus allowing you to save the information, would be very helpful in many cases.

We've been trying to get a molcalc server running on one of our workstations by following the instructions in the readme.rst. However, we're currently stuck on Step 7. After running

$ ./env/bin/pserve development.ini --reload

we get the following Trackback

Starting monitor for PID 1576308.
Traceback (most recent call last):
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/configparser.py", line 845, in items
    d.update(self._sections[section])
KeyError: 'molcalc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/hupper/ipc.py", line 319, in spawn_main
    func(**kwargs)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/hupper/worker.py", line 252, in worker_main
    func(*spec_args, **spec_kwargs)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/pyramid/scripts/pserve.py", line 30, in main
    return command.run()
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/pyramid/scripts/pserve.py", line 271, in run
    app = loader.get_wsgi_app(app_name, config_vars)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/plaster_pastedeploy/__init__.py", line 129, in get_wsgi_app
    global_conf=defaults,
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/paste/deploy/loadwsgi.py", line 253, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/paste/deploy/loadwsgi.py", line 278, in loadobj
    return context.create()
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/paste/deploy/loadwsgi.py", line 715, in create
    return self.object_type.invoke(self)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/paste/deploy/loadwsgi.py", line 152, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/site-packages/paste/deploy/util.py", line 55, in fix_call
    val = callable(*args, **kw)
  File "/home/cloudlab/Repositories/python/molcalc/molcalc/__init__.py", line 135, in main
    for k, v in parser.items(section):
  File "/home/cloudlab/Repositories/python/molcalc/env/lib/python3.7/configparser.py", line 848, in items
    raise NoSectionError(section)
configparser.NoSectionError: No section: 'molcalc'
Press ENTER or change a file to reload.

The error appears to be that the *.ini file needs a "molcalc" section, but we don't have enough context to guess what exactly is going on and what is needed.

We're very happy to provide as much information as we can to help, including details about the steps leading up to Step 7.

Thanks in advance!