Dear Amber users,
I'm still stuck with this issue. I cannot reproduce the following tutorial:
https://ambermd.org/tutorials/advanced/tutorial40/index.php in Amber22,
because the obtained .mrc files do not seem to work, I'm unable to
visualize the results in VMD. Can you please help me? I would like to be
able to use the .mrc files to visualize the density and then to be able to
use them again to position the molecules using this tutorial:
https://ambermd.org/tutorials/advanced/tutorial34/index.html
Best regards,
Karolina Mitusińska
wt., 19 mar 2024 o 18:13 Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> napisał(a):
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 25 2024 - 01:30:02 PDT
