From: Aashish Bhatt (aashish.ph16221_at_inst.ac.in)
Date: Mon Mar 02 2020 - 08:15:03 CST
Thank you for your response sir
I will be you look on this.
On Fri, Feb 28, 2020 at 8:16 PM Pawel Kedzierski <
> W dniu 28.02.2020 o 13:44, Aashish Bhatt pisze:
> Thank you sir for your response
> Can you please elaborate sir.
> I need to manually edit the charges or i am getting something wrong.
> Manually editing charges is bad science, they describe interactions in
> your system. You probably need to educate yourself more and then confirm
> with your scientific tutor/supervisor whether what you plan to do is
> sensible or not.
> You were advised to change which atom compose your QM part in such a way,
> that the partial charges of the entire QM region sum up to integer value.
> How to do it, depends on the parameters. For biological residues (amino
> acids, nucleotides) the charges should sum up to integer values for entire
> residue in any force field, so the QM/MM division on residue boundary
> should be safe. For arbitral molecules the charges will sum up to an
> integer value (the net formal charge) for the whole molecule.
> If one is calculating the parameters himself, the way is to add
> constraints to charge fitting to get the specified sum of charges within a
> fragment of the molecule. Such fragments define "charge groups" which dr
> Vermaas refers to; in CHARMM FF, the biological residues are already
> divided into relatively small charge groups which allows for better
> granularity of division in QM/MM context.
> It is possible to define charge groups using Amber Tools to parametrize
> arbitral molecules. Look up the "respgen" chapter in Amber Tools Manual for
> a start. Bear in mind, however, that if you impose nonsense constraints you
> will get nonsense charges so in general, you should set up a benchmark to
> test your parameters if they work well (that is, reproduce the properties
> of interest).
> With regards,
> Best Regards
> On Thu, Feb 27, 2020 at 8:31 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
>> Cut somewhere else between QM and MM regions. The errors are pretty
>> clear, in that it demands integer charges so that PME works. Amber
>> topologies do not have the "group" concept like CHARMM topologies do, so
>> the atomic charges within a molecule likely don't add to an integer.
>> On Thu, Feb 27, 2020 at 5:51 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
>>> Dear Sir/Ma'am
>>> I am trying to check bond breaking in my system with the help of QM/MM.
>>> I am getting the following error and i am using Amber topology.
>>> can you please look into it.
>>> *Info: 1) Group ID: 1 ; Group size: 9 atoms ; Total PSF charge:
>>> -0.412152 FATAL ERROR: QM atoms do not add up to a whole charge, which is
>>> needed for PME. ------------- Processor 0 Exiting: Called CmiAbort
>>> ------------ Reason: FATAL ERROR: QM atoms do not add up to a whole charge,
>>> which is needed for PME.*
>>> Best Regards
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