On Fri, Jul 17, 2020, Kliuchnikov, Evgenii wrote:
>
>Then I created tinker XYZ file:
>pdbxyz gag_wat
Look at this file with a text editor. Are all the atoms types 0? That is
typically the behavior when something goes wrong. But it's not always what
happens: basically we need to know if the error occurred here or later on.
If there is an error here, try a test of removing all the water molecules?
Does pdbxyz then seem to work?
Basically, I'm just trying to guess here, in the absence of more information.
But the first goal is to find out if pdbxyz and analyze "worked" or not, or
whether the problem is indeed in the tinker_to_amber step.
Caveat: others on the list use Amoeba more than I do. And, if the problem is
at the early stages (pdbxyz, analyze), you may need to ask at the tinker forum
as well.
.....dac
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Received on Fri Jul 17 2020 - 18:00:04 PDT
