From: Holly Freedman <hpfreedma.gmail.com>
Date: Tue, 29 Dec 2020 15:31:59 -0700

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
AMBER mailing list
Received on Tue Dec 29 2020 - 15:00:03 PST
Custom Search