Re: [AMBER] 5' Terminal Phosphate Parameters

From: Qinghua Liao <>
Date: Thu, 26 Jan 2017 15:57:06 +0100


Maybe the atom name of O5' is O5* in the lib or prep file.

You can have a check and modify it.

All the best,

On 01/26/2017 03:54 PM, Paul Meister wrote:
> Hello AMBER users,
> I am trying to run some MDs on a enzyme with a bound tRNA. I have tried to
> get parameters for the 5' terminal base with a phosphate using prepgen and
> the RED server, however there is always one atom that is not recognized,
> O5', the oxygen linking phosphate to the ribose. Does anyone know how to
> solve this problem or are there parameters for a terminal guanosine
> 5'-phosphate?
> Thank you all,
> Paul
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Received on Thu Jan 26 2017 - 07:00:05 PST
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