Hello Victor
A post processing would be necessary once you have the graphene structure
from charmm-gui.
Perhaps the following website might help.
https://github.com/IFM-molecular-simulation-group/HierGO
Thanks
Arun
On Fri, Dec 15, 2023 at 12:28 PM Victor Nazarychev <nazarychev.imc.macro.ru>
wrote:
> Hello, Arun!
>
>
>
> Thank you for your suggestion.
>
>
>
> However, as I understand, for the charmm-gui site automatically, only
> infinity graphene sheets could be built
> https://charmm-gui.org/?doc=demo&id=nanomaterial&lesson=9. There is no
> option to generate an infinitely long graphene oxide
>
>
>
> To automatically generate the graphene oxide topology you upload a pdb
> file of graphene oxide, but how do you include periodic box size in the
> pdb file?
>
>
> Best regards,
>
> Victor
>
> вт, 12 дек. 2023 г. в 13:09, Arun Srikanth <askforarun.gmail.com>:
>
>> Hello Victoria
>>
>> It is somewhat difficult. Usually what people do is to create a unit cell
>> and then use tlep. After that a custom script is used to create bonds
>> accross periodic boundaries.
>>
>> Have you tried using charmm gui. It gives you what you need but the force
>> filed is ofcourse charmm. Once you have got the file from charmm you can
>> easily change to gaff. I have tried it and let me know if you need any help
>>
>>
>> Thanks and regards
>> Arun
>>
>> On Tue, 12 Dec 2023, 9:48 am Victor Nazarychev via AMBER, <
>> amber.ambermd.org> wrote:
>>
>>> Dear Amber users,
>>>
>>> I simulate periodic molecular graphene oxide. I followed the tutorial at
>>> https://ambermd.org/tutorials/advanced/tutorial1_orig/, where the method
>>> for creating a topology for non-standard residues is discussed.
>>> I create .pdb files of my periodic molecules and prepare .lib files for
>>> every residue that I create from the GAFF force field.
>>>
>>> My question is, is it possible to automatically build a topology using
>>> tleap, where bonds, angles, dihedrals, and improper potential functions
>>> are
>>> written across periodic conditions?
>>>
>>> I found a tutorial
>>> https://ambermd.org/tutorials/advanced/tutorial13/Topology.php where the
>>> command "bond" is used to write a bond across the periodic image, but in
>>> this case, I should also manually write angles, dihedrals, and impropers?
>>> Is it possible to include in the .pdb file of my molecule information on
>>> periodic box size to automatically generate periodic topology? Perhaps
>>> another approach exists for writing bonded interactions across periodic
>>> boundary conditions?
>>>
>>> Best wishes,
>>> Victor
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Fri Dec 15 2023 - 05:30:02 PST
