Re: [AMBER] 5' Terminal Phosphate Parameters

From: Paul Meister <>
Date: Thu, 26 Jan 2017 14:28:19 -0500

Sorry for not being specific. The tRNA isn't bound through the phosphate
group, but is instead held to the protein through many hydrogen bonds. The
5' terminal phosphate is supposed to participate in the reaction. The PDB
ID for this protein is 2DXI. Running the files through LEaP, it tells me
that there are no parameters for OP3, a phosphate oxygen. The mol2 file
from RED shows me that it is there and bound. I'm just not sure why there
are parameters for the other two oxygen atoms, but not for OP3.

On Thu, Jan 26, 2017 at 12:21 PM, David Case <> wrote:

> 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.?
> or
> (b) There is an O5' atom in the R.E.D. unit that is not in the pdb file?
> or
> (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?
> ....dac
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Received on Thu Jan 26 2017 - 11:30:02 PST
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