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August 24, 2019

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WebMO Support Forum » Running WebMO Jobs » Job Options » Geometry optimization « Previous Next »

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Bedamoni
Unregistered guest
Posted on Monday, July 25, 2011 - 7:58 am:   

I have imported a gaussian input file(test.gjf) in WebMO, and I am unable to do geometry optimization(molecular mechanics calculation or semi-empirical)using MOPAC. MOPAC is already installed in the same machine(C:\Program Files\MOPAC\).Can you please tell me how can I submit that job in the MOPAC.
Thanking you in advance
JR Schmidt
Moderator
Username: Schmidt

Post Number: 189
Registered: 11-2006
Posted on Monday, July 25, 2011 - 8:51 pm:   

You need to configure MOPAC for use with WebMO. Login as user 'admin', go to the 'Interface Manager', and enable/configure MOPAC.
Anonymous
 
Posted on Tuesday, July 26, 2011 - 2:16 am:   

MOPAC is already enabled in the 'Interface Manager' despite the problem persists.
Thanking you
JR Schmidt
Moderator
Username: Schmidt

Post Number: 190
Registered: 11-2006
Posted on Tuesday, July 26, 2011 - 10:08 am:   

Can you be more specific as to what the problem is? What do you mean by the fact that you are "unable" to do a geometry optimization. What happens when you attempt the calculations?
Leigh_H
Unregistered guest
Posted on Tuesday, November 01, 2011 - 7:59 am:   

I have a similar problem, please could you offer advice? I too have MOPAC configured for use with Webmo within the interface manager but when I run a job the timer stays at 0, and the job status is 'Failed'. I have tested the same demo job on the buchner.chem demo site and it works ok. Also when I click on 'Raw output' it tells me that the webpage is unavailable. Any advice will be appreciated. Thanks, Leigh.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 201
Registered: 11-2006
Posted on Tuesday, November 01, 2011 - 12:39 pm:   

What version of MOPAC are you using? If using OpenMopac, please first run MOPAC (once) on the command line to "enable" it with the license key you should have received when you obtained OpenMOPAC.
Leigh_H
Unregistered guest
Posted on Tuesday, November 01, 2011 - 12:49 pm:   

Hi Schmidt, I am using Mopac2009. I have followed the instructions on the Webmo website and entered the license key, which then asked me if I accepted the regulations... or something!.. I'm guessing that the 'Raw output' link is not generating as the job is not running. Thank you for taking the time to get back to me :-)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 202
Registered: 11-2006
Posted on Tuesday, November 01, 2011 - 5:03 pm:   

When the job fails, attempt to view the job. In the "View Job" page, click the "all files" link on the left hand panel, and view the "run_log" file. Please post the contents of this file.
Leigh_H
Unregistered guest
Posted on Wednesday, November 02, 2011 - 6:14 am:   

I have clicked 'View Job' but am not getting an option for 'All Files' on the left. I tried the demo server and can see on there the link that you mean but it is not appearing on my system... :-(
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 10:56 am:   

Could it be that suexec is not configured correctly? I have tried looking for logs which indicate something to me but have been unable to find anything. I also read about a diagnose.pl script but that doesn't seem to work either. Sad times.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 203
Registered: 11-2006
Posted on Thursday, November 03, 2011 - 11:03 am:   

If you go to the 'Job Manager', select the failed job, and hit 'download' the 'run_log' file will be included in the archive for you to examine and post.
Will Polik
Moderator
Username: Polik

Post Number: 27
Registered: 7-2000
Posted on Thursday, November 03, 2011 - 11:28 am:   

The "All Files" link is a component of WebMO Pro and WebMO Enterprise, but it is not part of the free version of WebMO. That said, all the same information is available inside an archive.
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 11:46 am:   

Cheers both...

Cannot create directory /tmp/webmo-388/29: No such file or directory at /home/webmo/public_html/cgi-bin/webmo/run_mopac.cgi line 64.
Executing script: /home/webmo/public_html/cgi-bin/webmo/run_mopac.cgi
Script execution node: webmo.isd.glam.ac.uk

This is the run_log...
JR Schmidt
Moderator
Username: Schmidt

Post Number: 204
Registered: 11-2006
Posted on Thursday, November 03, 2011 - 11:52 am:   

Interesting. Can you please post the contents of your WebMO configuration file, 'globals.int' (located in the cgi-bin/interfaces directory).
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 11:57 am:   

Added as attachment, thanks again.
text/plainglobals.int
globals.txt (1.3 k)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 205
Registered: 11-2006
Posted on Thursday, November 03, 2011 - 12:00 pm:   

I am curious whether for some reason your system is configured such that WebMO (or CGI applications running under Apache) cannot write to the /tmp directory. What are the permissions on /tmp (ls -alF /tmp)?
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 12:04 pm:   

text/plainPermissions
ls -alF tmp.txt (0.6 k)
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 12:08 pm:   

I just temp changed the permissions on /tmp to 777, the job ran but still failed... Sorry for being such a noob
text/plainrun_log
run_log.txt (0.2 k)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 206
Registered: 11-2006
Posted on Thursday, November 03, 2011 - 12:17 pm:   

I see the issue. The permission on BOTH /tmp AND /tmp/webmo are wrong.

/tmp on ANY system should always be world writable. In particule, use:
chmod 1777 /tmp
(Note the 1, which is important in this case).

/tmp/webmo should be just world writable,
chmod 777 /tmp/webmo

Some external agent changed all these permissions, which is not good!
Leigh_H
Unregistered guest
Posted on Thursday, November 03, 2011 - 12:24 pm:   

Schmidt that has worked, thank you so much for the help you have given me, you are now on my Christmas card list :-)
George Richter
Unregistered guest
Posted on Thursday, November 13, 2014 - 12:33 pm:   

I am relatively new to WebMO. When starting a new job (e.g, MOs) using a previous WebMO GeometryOptimization job by clicking "New Job Using this Geometry", does one need to manually include the previous CheckPoint file if saved, or does this "New Job Using this Geometry" override the need to manually include a CheckPoint file in the input file?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 431
Registered: 11-2006
Posted on Thursday, November 13, 2014 - 3:46 pm:   

No checkpoint is required when doing "New Job with this Geometry". But saving/using a checkpoint file can make things for efficient, in terms of re-using the converged SCF.
George Richter
Unregistered guest
Posted on Thursday, November 13, 2014 - 4:23 pm:   

Thanks, Schmidt! This is very helpful!
I tried getting some info from the manual on how to use a previous CHK file for a new calculation. Do I input/type this as a separate line in the input file (e.g., %CHK=previous.chk) or do I simply use the job number in the job line
(e.g., # B3LYP/gen OPT 12173 nosymm etc)
where "12173" is the previous completed job. Or is there a section of the manual/web you can point me to? Any help you can give will be most appreciated. Sorry if this is too much of a "basic question".
JR Schmidt
Moderator
Username: Schmidt

Post Number: 432
Registered: 11-2006
Posted on Thursday, November 13, 2014 - 4:25 pm:   

If you have selected the option to "Save Checkpoint" in advanced job options, you can then "Use Checkpoint File" in a later job (also in Advanced Job Options)
George Richter
Unregistered guest
Posted on Thursday, November 13, 2014 - 4:31 pm:   

Ahh. Found it. Thanks so much!
shafaq
Unregistered guest
Posted on Friday, June 12, 2015 - 8:19 am:   

Hi, I am supposed to run two Gaussian calcualtions
1. geometry optimization using B3LYP which is quite straight forwar and i saved the checkpoint file as well and found it simple to run.
2. Next on this geometry i have to run a second Gaussian job using HF level theory and do single point energy calcualtion for which i have to modify the input file. But the job fails because when in advanced options the area where you can select the checkpointfilename, that job name doesnt appear and the job fails and output says that no Z-matrix is found on the checkpoint file. {The secobnd job ran correctly for those jobs for which i could select my previous job as "use checkpoint file in advanced options" }
Can you please help me with this?
John Keller
Unregistered guest
Posted on Wednesday, June 17, 2015 - 3:59 am:   

There is no need to use the chkpt file in this case. Open the results page of the B3LYP job, click New Job Using This Geometry. Click Continue, Choose Gaussian, Molecular Energy, HartreeFock, your basis set, charge, multiplicity. Then click continue. See jobs 198923 and 198924 on the WebMO Demo server (H2O, 6-31G* basis)

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