Dear AMBER mailing list,
I am trying to model cytidine monophosphate base-paired with
guanosine monophosphate (i.e. a single RNA base-pair), and I could use some
advice on how best to do this please.
I noticed that you have two libraries that might be helpful,
namely terminalphos.LJbb-RNA.lib and terminal_monophosphate.lib. With the
former of these, leap gives me missing parameters errors:
Error: For atom (.R<CMP 1>.A<O4' 10>) could not find vdW (or other)
parameters for type (OR)
Where are these missing parameters? What is the terminalphos.LJbb-RNA.lib
library meant to be used for?
Also for both of these two libraries, the H atoms do not get added to the
3' oxygen atoms causing non-integral charges. How can I stipulate that the
hydrogen atom be added on the 3' O atom?
Thank you for your time looking at my problem.
Holly Freedman
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Received on Tue Dec 29 2020 - 15:00:03 PST
