From: M. A (matabay2010_at_gmail.com)
Date: Sat May 09 2020 - 01:55:18 CDT
Dear Mariano
Hi
I don't know how I can be thankful for your helps. It worked. Thank you
very much, you are great!.
Bests
On Fri, May 8, 2020 at 8:44 PM Mariano Spivak <marspivak_at_gmail.com> wrote:
> Hi,
>
> The error you got is due to a problem while running the QM software, in
> this case it is MOPAC. Check the line "ERROR: Could not find QM output
> file!", that tells you that the QM program did not finish correctly.
> Now let's try to understand what was the problem. Whenever you have such a
> problem, you should first go to the QM output file which is in the
> directory defined by qmBaseDir and in the 0 folder.
> So if you go to qmmm_exec/QMMM-Min/0 you will find there are two files:
> qmmm_0.input is the input file for MOPAC
> qmmm_0.input.out is the output file for MOPAC
> the latter tells you there was a problem with the simulation:
>
> Faulty atom: 324
>
>
> Faulty line: " 84.338000 1 99.710000 1 92.849000 1"
>
>
> Unless MINI is used, optimization flags must be 1, 0, or -1
>
>
> If the geometry is in Gaussian format, add keyword "AIGIN" and
> re-run
>
>
>
> ******************************************************************************
>
> *
> *
>
> * Error and normal termination messages reported in this calculation
> *
>
> *
> *
>
> * Unless MINI is used, optimization flags must be 1, 0, or -1
> *
>
> * JOB ENDED NORMALLY
> *
>
> *
> *
>
>
> ******************************************************************************
>
>
>
> The highlighted line says one of the lines in the qmmm_0.input file is
> missing the atom element.
> Check the qmmm_0.input file, all the lines should have the atom element
> first:
>
> N 76.820000 1 95.154000 1 91.396000 1
>
> H 76.060000 1 94.883000 1 90.789000 1
>
> H 76.895000 1 94.813000 1 92.344000 1
>
> C 81.514000 1 99.934000 1 92.011000 1
>
> 80.617000 1 99.928000 1 92.453000 1
>
> O 81.520000 1 100.542000 1 90.717000 1
>
> 81.321000 1 99.948000 1 89.989000 1
>
> C 82.509000 1 100.618000 1 92.925000 1
>
> 82.002000 1 100.935000 1 93.727000 1
>
> O 83.197000 1 101.651000 1 92.216000 1
>
> H 83.862000 1 101.198000 1 91.683000 1
>
> C 83.700000 1 99.561000 1 94.860000 1
>
> 83.472000 1 100.489000 1 95.155000 1
>
> 83.150000 1 98.807000 1 95.219000 1
>
> O 85.071000 1 99.309000 1 95.142000 1
>
> ....
> but there are a few lines that have the first letter missing, now this
> problem comes from the file qm-input.pdb which has some missing elements
> for the last column.
> for example, search for the highlighted coordinates in qm-input.pdb, you
> will find those are missing the element column.
>
> So you need to fix the qm-input.pdb file so that all the atoms have the
> element column, after that it should work.
>
> Best
>
>
>
> On Tue, May 5, 2020 at 2:29 AM M. A <matabay2010_at_gmail.com> wrote:
>
>> Dear Mariano
>> Hi
>> Thank you very much for your helps. finally I finished my test run and I
>> did qmmm simulation of tutorial file with your guidance. Now I am trying to
>> run my own qmmm simulation. After preparing input files I checked every
>> thing but I faced a problem again: the error is:
>> TCL: Minimizing for 1000 steps
>> Info: List of ranks running QM simulations: 0.
>> ERROR: Could not find QM output file!
>> FATAL ERROR: (unknown error): No such file or directory
>> [Partition 0][Node 0] End of program
>> I don't know what is this error because I have very little information
>> about DFT
>> I sent folder of my input files. A.pdb is the qm region. could you look
>> at them and tell me what the problem is?
>> I am very very grateful for your helps
>> bests
>>
>> On Mon, Apr 27, 2020 at 6:53 PM Mariano Spivak <marspivak_at_gmail.com>
>> wrote:
>>
>>> Regarding the energies.dat file, it looks correct which means gnuplot
>>> should open it. what error is gnuplot giving you? You can also use excel or
>>> a similar program to load the data in energies.dat and plot the data.
>>> In terms of the RMSD analysis, you should be able to do that in VMD by
>>> using the dcd file of your simulation, as RMSD does not care whether the
>>> simulation was QM/MM or MM.
>>> Try using the RMSD tools present in VMD -> Extensions -> Analysis. Check
>>> the tutorials for those.
>>>
>>> Thanks
>>>
>>> On Sat, Apr 25, 2020 at 5:18 AM M. A <matabay2010_at_gmail.com> wrote:
>>>
>>>> Hi Mariano
>>>> Thank you for your helps, they are really useful. my problem is that
>>>> for executing qmmm simulation I have to use the server of our university.
>>>> So I can't use qwikmd plugin there because vmd is a visualization
>>>> computer program and I cant open it in my home at server. Therefore I
>>>> prepared conf file and md and qm commands for qmmm simulation.
>>>> I did your suggestions and prepared energies.dat file but gnuplot can't
>>>> open it. could you help me please?
>>>> I sent both .log and .dat files
>>>> I have a suggestion as well: in part of advanced analysis of qwikmd
>>>> there is not rmsd. as you know it is important for protein structure. if it
>>>> is possible for you please add this part because for example it is
>>>> necessary for me as a user.
>>>> best regards
>>>>
>>>> On Mon, Apr 20, 2020 at 7:20 PM Mariano Spivak <marspivak_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> The NAMD Plot plugin currently does not work with QM/MM simulation log
>>>>> files.
>>>>> I can work on that but it is not top of my priority list. Remember
>>>>> that you have the option to work with QwikMD, which will help with the
>>>>> analysis.
>>>>>
>>>>> In VMD, you can still analyze the QM/MM trajectory by loading the psf,
>>>>> pdb and dcd files.
>>>>>
>>>>> In order to get energies, one option is to work outside of VMD, either
>>>>> using python or grep and gnuplot.
>>>>> for example:
>>>>> grep QMENERGY logfile > energies.dat
>>>>> then in gnuplot: p 'energies.dat' u 2:4 w l
>>>>>
>>>>> Hope this helps
>>>>>
>>>>> On Mon, Apr 20, 2020 at 5:21 AM Francesco Pietra <
>>>>> chiendarret_at_gmail.com> wrote:
>>>>>
>>>>>> Hi Maryam
>>>>>> Did you submit the general dcd or QMonly.dcd?
>>>>>>
>>>>>> cheers
>>>>>> fp
>>>>>>
>>>>>> On Mon, Apr 20, 2020 at 11:02 AM M. A <matabay2010_at_gmail.com> wrote:
>>>>>>
>>>>>>> Dear al,
>>>>>>> Hi
>>>>>>> For learning qmmm simulation I tried to repeat the related tutorial
>>>>>>> and it was executed correctly.
>>>>>>> Now I have a question:
>>>>>>> Actually in addition qm analysis for atoms of QM region, I want to
>>>>>>> check thermodynamic properties of residues around QM region. So after
>>>>>>> simulation and in any part of simulation for example Minimization,
>>>>>>> Annealing or QMMM, I uploaded structure files(CBM_QM_QwikMD.pdb and
>>>>>>> CBM_QM_QwikMD.psf) and dcd files for analyzing thermodynamic properties
>>>>>>> like energy, temperature or RMSD .... with NAMD PLOT plugin or other
>>>>>>> plugins of vmd, but after uploading log file there was nothing in
>>>>>>> multiplot window and this window was empty. while log file shows that
>>>>>>> simulation is completed and there is data of energy and pressure.
>>>>>>> do you know what the problem is?
>>>>>>> I am grateful for your help.
>>>>>>>
>>>>>>> best regards
>>>>>>>
>>>>>>> --
>>>>>>> Maryam Atabay
>>>>>>> Ph.D in Nano Computational Chemistry
>>>>>>> Department of Physics, Sharif University of Technology
>>>>>>>
>>>>>>>
>>>>
>>>> --
>>>> Maryam Atabay
>>>> Ph.D in Nano Computational Chemistry
>>>> Department of Physics, Sharif University of Technology
>>>>
>>>>
>>
>> --
>> Maryam Atabay
>> Ph.D in Nano Computational Chemistry
>> Department of Physics, Sharif University of Technology
>>
>>
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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