From: M. A (matabay2010_at_gmail.com)
Date: Sun Mar 08 2020 - 04:30:03 CDT
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
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