Dear Prof. Case,
Thanks for your response. As you said, it is compatible with OL15. I was
able to use that. Is there any suggestions for changes to make so that I
could use it with bsc1?
_Sruthi
On Sat, 14 Jun, 2025, 11:21 David A Case, <dacase1.gmail.com> wrote:
> On Fri, Jun 13, 2025, Sruthi Sudhakar via AMBER wrote:
> >
> >I am working on a DNA-RNA hybrid structure. While I load my pdb structure
> >using the following combination, I get the error:
> >source leaprc.water.tip3p
> >source leaprc.DNA.bsc1
> >source leaprc.RNA.OL3
> >loadoff terminal_monophosphate.lib
> >nuc=loadpdb nuc.pdb
> >saveamberparm nuc nuc.prmtop nuc.inpcrd
>
> My suspicion is that terminal_monophosphate.lib is not fully compatible
> with
> DNA.bsc1. As an experiment, can you try DNA.OL24 (or DNA.OL15) instead?
>
> If I am correct, it will probably take some file editing to get what you
> want.
>
> ....dac
>
>
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Received on Sat Jun 14 2025 - 12:00:02 PDT
