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

From: M. A (matabay2010_at_gmail.com)
Date: Fri Apr 17 2020 - 12:06:08 CDT

Dear Mariano
Hi
Thank you so much. Finally I solved the problem. I checked the directory
that I used for qmBaseDir and also MOPAC program was correctly installed.
But problem was because of qm-input.pdb. when I prepared 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 wasn't this column( I mean the last column in
pdb file). when I put it in qm-input.pdb, it worked and QM simulation was
done. Now I have another question:
in qmmm simulation 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 the log file there
was nothing in multiplot window and this window was empty. Actually in
addition qm analysis for atoms of QM region, I want to check thermodynamic
properties of residues around QM region. do you know what the problem is?
I am grateful for your help.

best regards

>
> 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

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST