On Tue, May 23, 2023, Robert Heße via AMBER wrote:
>Am 2023-05-22 18:18, schrieb Rodrigo Galindo-Murillo:
>>As far as I can see, you do not need an frcmod file, I ran your
>>molecule through tleap and it generated the topology and coordinates
>>just fine.
>
>thank you for the fast response. As far as i know it should be an
>already defined residue as i am saving it directly from the OL15 force
>field via tleap. For the future i wanted to incoperate modified
>nucleobases based on the DG of OL15, which i most likely have to
>parametrize. As such i wanted to compare them with an already
>established residue but i fear that the parametrization might not be
>possible without defining the missing atom types somehow.
I would still wait to see what parameters are missing in your modified
bases. If something is missing (without running parmchk), you may be able
to hand-create a frcmod file based on analogies to what is in gaff2.dat.
....dac
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Received on Tue May 23 2023 - 10:30:02 PDT
