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
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Received on Tue Dec 12 2023 - 02:30:02 PST
