From: M. A (matabay2010_at_gmail.com)
Date: Sun Mar 08 2020 - 05:09:07 CDT
Hi
Sorry I asked my question wrongly. my question is:
In qm-input.pdb file of tutorial for some atoms the occupancy and beta is
1.00 1.00.
I don't know which atoms are included in?
That will be very kind of you if you tell me the reason because I don't
know how I should use it for atoms of my structure.
Best regards
On Sun, Mar 8, 2020 at 1:00 PM M. A <matabay2010_at_gmail.com> wrote:
> Dear Mariano
> Hi
> I corrected my pdf file as you guided me. In my pdb file occupancy is
> 0.00 except to the QM and MM atoms involved in the bond, and beta for QM
> region is 1.00. Now I have a question: In qm-input.pdb file of tutorial for
> some atoms the occupancy and beta is 1.00 0.00.
> I don't know which atoms are included in?
> That will be very kind of you if you tell me the reason because I don't
> know how I should use it for atoms of my structure.
>
> Best regards
>
> On Tue, Feb 25, 2020 at 1:53 PM M. A <matabay2010_at_gmail.com> wrote:
>
>> Dear Mariano
>> Hi
>> At first I am very thankful for your guidance. I understood that what
>> problem is and I will try it. I hope it will work.
>> Best Regards
>>
>> On Mon, Feb 24, 2020 at 12:27 AM Mariano Spivak <marspivak_at_gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> The error comes from your qm-input.pdb file, the occupancy column of the
>>> pdb is full of 1.00. The occupancy column must be 0.00 for all atoms except
>>> those involved in a QM-MM bond.
>>> To solve this, you can use VMD and type in the console:
>>> mol load psf ionized.psf pdb qm-input.pdb
>>> [atomselect top all] set occupancy 0.00
>>> [atomselect top all] writepdb newqm-input.pdb
>>>
>>> Assuming the beta column of the pdb correctly defines the QM atoms, you
>>> must check the QM-MM bonds and set occupancy 1.00 to the QM and MM atoms
>>> involved in the bond.
>>>
>>> Best
>>>
>>> On Sat, Feb 22, 2020 at 3:35 AM M. A <matabay2010_at_gmail.com> wrote:
>>>
>>>> Dear Mariano
>>>> Hi
>>>> I agree with you and I had done it but unfortunately I still have
>>>> problems. As you asked me I sent the pdb file and attached
>>>> both the original pdb file and the qm-input.pdb file.
>>>>
>>>> Stay Awesome
>>>> Maryam
>>>>
>>>>
>>>>
>>>> On Wed, Feb 19, 2020 at 11:05 PM Mariano Spivak <marspivak_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> The error message indicates there is a problem in the assignment QM-MM
>>>>> bonds, which are given in the qm-input.pdb file.
>>>>> If you intended to have bonds between QM and MM atoms, check the
>>>>> following in the qm-input.pdb file:
>>>>> (assuming that "qmColumn beta" and "qmBondColumn occ" in the config
>>>>> file)
>>>>> The QM atom(s) with the bond(s) have 1.00 1.00 in the occupancy beta
>>>>> columns
>>>>> The MM atom(s) with the bond(s) have 1.00 0.00 in the occupancy beta
>>>>> columns
>>>>>
>>>>> If you still have problems, you can send me the pdb file and I can
>>>>> give it a look
>>>>>
>>>>> Best
>>>>>
>>>>> On Sun, Feb 16, 2020 at 12:48 AM M. A <matabay2010_at_gmail.com> wrote:
>>>>>
>>>>>>
>>>>>> Dear All,
>>>>>> I want to execute the QM/MM simulation through NAMD and ORCA. The
>>>>>> structure was equilibrated before. Then I tried to do QM/MM. But
>>>>>> unfortunately at the first steps, I faced this error:
>>>>>>
>>>>>> Info: Using the following PDB file for QM parameters: qm-input.pdb
>>>>>> Info: Number of QM atoms (excluding Dummy atoms): 329
>>>>>> ERROR: Atoms 0 and 4 are assigned as MM atoms.
>>>>>> FATAL ERROR: Error in QM-MM bond assignment.
>>>>>>
>>>>>> could you help me please to solve this problem?
>>>>>>
>>>>>> Best Regards
>>>>>> Maryam
>>>>>> --
>>>>>> 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
>
>
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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