Re: FATAL ERROR: Error running command for QM forces calculation.

From: M. A (matabay2010_at_gmail.com)
Date: Fri Apr 17 2020 - 11:53:08 CDT

Dear Mariano
Hi
I am grateful for your help. Finally I solved the problem. I checked the
directory that I used for qmBaseDir and MOPAC program was correctly
installed. But problem was because of qm-input.pdb. when I prepare this
file I used structure pdb file, and in this file there isn't the element
column and so in my qm-input.pdb file there was'nt this column( I mean the
last column in pdb file). when I put it in qm-input.pdb, it worked and and
QM simulation was done. Now I have another question:
after simulation and in any part of simulation foe example Minimization,
Annealing or QMMM I uploaded structure files(CBM_QM_QwikMD.pdb and
CBM_QM_QwikMD.psf) and dcd file for analysing thermodynamic properties like
energy, temperature and .... with NAMD PLOT pugine, but after uploading the
log file there is nothing in multiplot window and I saw nothing. because I
want to check thermodynamic properties in MD simulation for residues around
QM region in addition qm analysis for

On Tue, Apr 7, 2020 at 10:04 PM Mariano Spivak <marspivak_at_gmail.com> wrote:

> Hi,
>
> The error most likely suggest that the ORCA/MOPAC simulation is not
> working. Check the directory that you used for qmBaseDir, there should be
> files for the QM simulation.
> First of all, check the file qmmm_0.input was created, this is the file
> NAMD prepares for the QM to run. If so, check the file qmmm_0.input.out is
> there, this is the output file of the QM simulation.
> In the file qmmm_0.input.out you should find any issues with the QM
> simulation, for example convergence problems, wrong charge/multiplicity,
> etc.
> If the file qmmm_0.input.out is not present, that could mean that the
> ORCA/MOPAC program is not correctly installed, or is missing the link to
> the libraries. Try running the program outside of NAMD, using the
> qmmm_0.input file as input and report here any errors you might find.
>
> Best
>
> On Tue, Apr 7, 2020 at 12:09 PM M. A <matabay2010_at_gmail.com> wrote:
>
>> Dear All,
>> Hi
>> I am trying to repeat simulation of qm/mm tutorial file (4b9f pdb). I
>> don't want to use QwikMD plugin. At fires I executed MD part successfully
>> but when I wanted to execute qm/mm part I faced this problem:
>> FATAL ERROR: Error running command for QM forces calculation.
>> I prepared qm-input file so
>> I used this command to select qm region:
>> within 5 of (resname CAL)
>> and then I gave beta=1.00 to all atoms of qm region and occupancy=1.00 to
>> all mm atoms ( I mean to CA and C atoms of residue which is located exactly
>> before the qm region and also to CA and C atoms of the last residue). I
>> can't understand what the problem is because I used all config files of
>> tutorial.
>> 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

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