Hi,
I’m not entirely sure what is being asked here, however, if you’re simply
wishing to conduct an MD simulation of your peptidoglycan, connecting the
multiple fragments via the tleap bond function should be fine. Be sure to
save off test topology and starting trajectory files to ensure your
connectivities are nominal.
Additionally, certainly ensure that you have selected the correct/proper
force fields and libraries that adequately describe the properties of your
system and the various macromolecules associated.
Best of luck,
Kyle W
Memorial University of Newfoundland
On Mon, Nov 18, 2024 at 20:02 Angelo Gallo via AMBER <amber.ambermd.org>
wrote:
> Dear Amber users and developers,
>
> I have a question. I have N-Acetylated Muramic Acid and N-Acetylated
> Glucosamine. They are connected together and 5 amino acids are also
> attached and phosphate and lipid too.
>
> Which is the best way to proceed?
>
> I tried to generate in gaussian the N-Ac Muramic acid and the N-Ac
> Glucosamine modified with the phosphate and lipid and then connect the two
> of them with the pentapeptide using the bond function
>
> Any better suggestions?
>
> Thanks a lot
>
> Best regards
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Received on Tue Nov 19 2024 - 09:00:02 PST
