On Tue, Jan 07, 2025, Kankana Bhattacharjee via AMBER wrote:
>
>I used opc3pol water model in my simulation and for that I loaded the
>following commands in my initial set-up used by leap tool.
>These are:
>source leaprc.water.opc3pol
>loadAmberParams frcmod.opc3pol_HMR4fs
>Then, used gaff2 f for pyrrole one. Performed MM set-up and while running
>QM-MM set-up I am getting the following error as:
>Unable to correctly identify element O
>Note: element guessing does not work with Hydrogen
> Mass Repartitioning if ATOMIC_NUMBER is not
> present in the topology file
>
There are two problems here:
1. You are telling us what you intended to do ("perform MM setup") and not
what you actually did (i.e. the actual commands and input being used.) This
makes it very hard to figure out how to help. We don't even know the
context of the error message: what program was running? How far did it get
before emitting that message? etc.
2. Posting to this list should not be your first impulse. At best, it takes
days to post and get a reply. Plus, people will be more inclined to help if
you show evidence of how to tried to debug this yourself. For example, does
it depend on using the opc3pol water model? Would a more standard water model
(or no water model) work better? Did you try leaving out the
"loadAmberParams frcmod.opc3pol_HMR4fs" step?
...good luck....dac
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Received on Tue Jan 07 2025 - 09:30:02 PST
