Dear Amber users,
I was trying to use Amber22 rism3d.snglpnt to follow the tutorial on
calculating ion distributions around DNA molecule
https://ambermd.org/tutorials/advanced/tutorial40/index.php but
unfortunately I'm unable to reproduce it.
I'm able to obtain the set of files from 1D-RISM calculations, and the
rism3d.snglpnt command also produces some output files, but they are
incorrect, as I'm unable to visualize them in VMD. I tried with the
g.O.1.mrc file which I downloaded from the tutorial website and it worked
(I was able to visualize the density map in VMD).
I tried to use Amber20 (installed via conda), and I got the working files
(but with different extensions, as expected).
Can you please tell me what to do to get Amber22 output working files? Then
I want to use the files to reproduce another tutorial to obtain positions
of water molecules around the molecule -->
https://ambermd.org/tutorials/advanced/tutorial34/index.html
Looking forward to hearing from you!
Best regards,
Karolina Mitusińska
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Received on Tue Mar 19 2024 - 10:30:02 PDT
