Re: [AMBER] 5' Terminal Phosphate Parameters

From: David Case <>
Date: Thu, 26 Jan 2017 12:21:00 -0500

On Thu, Jan 26, 2017, Paul Meister wrote:
> 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?

Can you be more specific? Is the "bound tRNA" bound through the 5' terminal
phosphate group? Are you starting from a PDB file from the wwPDB? If so,
what is its ID?

Second, when you say that "there is one atom that is not recognized, O5'", do
you mean

   (a) There is an O5' atom in the pdb file that is not in the unit you
       created with R.E.D.?


  (b) There is an O5' atom in the R.E.D. unit that is not in the pdb file?


  (c) something else?

Finally, Francois and others that the R.E.D. site are generally very willing
to help users. Have you asked for help there?


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Received on Thu Jan 26 2017 - 09:30:03 PST
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