VMD-L Mailing List

From: Mariano Spivak (mariano_at_ks.uiuc.edu)
Date: Thu Sep 30 2021 - 11:17:33 CDT

Hi Bassam,

If you don’t mind sharing (privately) the files you used (psf, pdb, par, ORCA files), I can check the error and try to come up with a solution.

Thanks

> On Sep 30, 2021, at 11:07 AM, Bassam Haddad <bhaddad_at_pdx.edu> wrote:
>
> Hi Mariano,
>
> I was able to make it through the tutorial without any problems, however I am encountering an odd error when I attempt to paramaterize salicylate.
>
> I can make it through the second ORCA step, and then ffTK fails at the water-optimization step with the following error:
>
> "measure fit: selections must have the same number of atoms"
>
> I've checked all of the outputs from ORCA and they all contain 18 atoms (15 from SAL + 3 from water) so I am having trouble pinning down the source of the error -- the first base-water.psf/pdb that is generated also has 18 atoms, so again I am not sure where the error is coming from.
>
> Any insite/suggestions you or anyone else has for me would be greatly appreciated.
>
> Best,
> Bassam
>
> On Tue, Sep 28, 2021 at 9:43 PM Mariano Spivak <mariano_at_ks.uiuc.edu <mailto:mariano_at_ks.uiuc.edu>> wrote:
> Hi Bassam,
>
> Sorry for delayed reply, we had a very busy week.
>
> Could you check if the ORCA run generated a file that ends with *_job2_internal.hess?
> You should be able to use the hess.out in FFTK without any issue.
> The error you see in the hess.out file occurs in the job2 run, which is there only to obtain the hessian in internal coordinates. So no need to worry about that error, sorry for the confusion.
>
> Let me know if you encounter any other issues.
>
> Best
>
>> On Sep 27, 2021, at 7:43 AM, Bassam Haddad <bhaddad_at_pdx.edu <mailto:bhaddad_at_pdx.edu>> wrote:
>>
>> Hi Mariano,
>>
>> I got the same error as mentioned above, even when running orca on the example hess.inp file from your ks.uiuc web-page. I am at a loss for how to get this optimization to work, do you have an idea of what I can do to increase the maxiter as the program requests? Furthermore I have the same error when using ORCA_4.1.1 and ORCA_5.0.0. Below I have attached the input and output files.
>>
>> Thank you,
>> Bassam
>>
>> On Tue, Sep 21, 2021 at 8:15 PM Bassam Haddad <bhaddad_at_pdx.edu <mailto:bhaddad_at_pdx.edu>> wrote:
>> Hi All,
>>
>> ORCA is terminating early due to lack of convergence in the geometry optimization calculation during step-4 (4-baOpt). I tried increasing the 'maxiter' in the ETOH.hess.inp file, however it fails every time regardless of how high i set it. When I do run the calculation, it notifies me that it's setting the maxiter to 0, regardless of what I put as the max iteration.
>>
>> I have attached my input and output from my failed run.
>>
>> I appreciate any help you can provide.
>>
>> Thanks,
>> Bassam
>>
>> On Tue, Sep 21, 2021 at 5:34 PM Bassam Haddad <bhaddad_at_pdx.edu <mailto:bhaddad_at_pdx.edu>> wrote:
>> Hi Mariano,
>>
>> Thank you for your reply. I was able to resolve the issue by installing orca_4.1.1 (the version in the ffTK tutorial). My issues were with orca_5.0.0.. I hadn't run anything differently, so I assume it was an error due to version differences.
>>
>> Best,
>> Bassam
>>
>> On Sun, Sep 19, 2021 at 8:20 PM Mariano Spivak <mariano_at_ks.uiuc.edu <mailto:mariano_at_ks.uiuc.edu>> wrote:
>> Hi Bassam,
>>
>> The bond/angle optimization step in FFTK using ORCA generates one input file (e.g. hess.inp) that contains two calculations in sequence, the file “initial.hess” is generated by the first calculation.
>> The error you see ORCA report is most likely due to from some error termination in the first calculation (e.g. issues with memory, not converged).
>> Try repeating the calculation or you can send the generated files and I can take a look at the issue.
>>
>> Hope this helps.
>>
>> Best
>>
>>> On Sep 18, 2021, at 11:02 AM, Bassam Haddad <bhaddad_at_pdx.edu <mailto:bhaddad_at_pdx.edu>> wrote:
>>>
>>> Hello again,
>>>
>>> In an attempt to trouble-shoot my previous problems, I performed the ffTK tutorial using the .psf/.pdb/.par from the tutorial files. The charge optimization step worked, which tells me that there is an issue with the way that CHARMM-GUI generated the .psf of my ligand.
>>>
>>> I did however run into another problem, however, while running the tutorial files (ETOH). When I went to run the bond and angle optimization, ORCA threw an error saying it needed "initial.hess" as an input and could not find it. "initial.hess" is not generated when using the "Write QM Inputs" function in the ffTK GUI. Where can we find/build initial.hess for our own calculations?
>>>
>>> Thank you for your time!
>>>
>>> Bassam
>>>
>>> On Mon, Sep 13, 2021 at 12:38 PM Bassam Haddad <bhaddad_at_pdx.edu <mailto:bhaddad_at_pdx.edu>> wrote:
>>> Hello All,
>>>
>>> I am currently trying to parameterize a small molecule using fftk on vmd_1.4a51, with ORCA, and I ran into an error preceding charge optimization:
>>>
>>> `ERROR) No molecules loaded.mol addfile operates on one molecule only`
>>>
>>> Though the .psf and .pdb are loaded. All ORCA inputs were generated in ffTK, and orca ran without error. I have seen this error pop-up on the mailing list before  <https://tcbg.illinois.edu/Research/vmd/mailing_list/vmd-l/32301.html>however it appears to be an unrelated issue, as I am not using Gaussian, and don't appear to have errors from ORCA. I would appreciate any assistance you can provide in overcoming this error.
>>>
>>> I have attached the error logs.
>>>
>>> Thank you for your time!
>>>
>>> ________________________
>>> Bassam Haddad, Ph.D.
>>> Post-Doctoral Researcher
>>> Forschungszentrum Juelich
>>>
>>
>> <hess.inp><hess.out>
>
> <chargeOpt.0.debug.log><chargeOpt.0.error>