From: M. A (matabay2010_at_gmail.com)
Date: Tue Feb 25 2020 - 04:23:19 CST
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.
On Mon, Feb 24, 2020 at 12:27 AM Mariano Spivak <marspivak_at_gmail.com> wrote:
> 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.
> On Sat, Feb 22, 2020 at 3:35 AM M. A <matabay2010_at_gmail.com> wrote:
>> Dear Mariano
>> 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
>> On Wed, Feb 19, 2020 at 11:05 PM Mariano Spivak <marspivak_at_gmail.com>
>>> 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
>>> The MM atom(s) with the bond(s) have 1.00 0.00 in the occupancy beta
>>> If you still have problems, you can send me the pdb file and I can give
>>> it a look
>>> 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 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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