From: M. A (matabay2010_at_gmail.com)
Date: Sat Mar 14 2020 - 17:17:37 CDT
Hi
As you mentioned I corrected occupancy and beta for QM and MM atoms, but
unfortunately I face this error yet.
Info: Using the following PDB file for QM parameters: qm-input.pdb
Info: Number of QM atoms (excluding Dummy atoms): 330
ERROR: Atoms 831 and 833 are assigned as QM atoms.
FATAL ERROR: Error in QM-MM bond assignment.
it will be kind of you if you help me to solve it.
Best Regards
On Mon, Mar 9, 2020 at 11:06 PM Mariano Spivak <marspivak_at_gmail.com> wrote:
> The atoms with occupancy 1.00 and beta 1.00 are QM atoms involved in a
> bond with a MM atom.
> According to your email, you should have this in your pdb.
> Do you have an error in your simulation?
>
> On Sun, Mar 8, 2020 at 5:09 AM M. A <matabay2010_at_gmail.com> wrote:
>
>> 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
>>
>>
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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