Re: [AMBER] parameter file for dUTP

From: David Case <>
Date: Fri, 31 May 2019 01:43:37 +0000

On Fri, May 31, 2019, sunyeping wrote:
>Thank you for the help. Actually I am very new to amber. Could you tell
>me what is the RNA force field file containding du and where can I find

You have to play Frankenstein here: I'd start with the triphosphates
from the contributed parameters database (i.e. the Carlson parameters);
then subsitute the sugar and base from dT in place of the sugar and base
from G; then remove the methyl group to turn dT -> dU.

[Above is the equivalent of taking Zachary's dTTP and removing the
methyl group on the base. You might try contacting him off-line to see
if he has files to share.]

...good luck....dac

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Received on Thu May 30 2019 - 19:00:03 PDT
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