Re: [AMBER] 5' Terminal Phosphate Parameters

From: FyD <>
Date: Fri, 27 Jan 2017 07:47:42 +0100

Dear Paul,

"When describing the problem you encountered with R.E.D. Server
Development, please also provide the 'PXXXX' R.E.D. Server Development
job name in the body of your email so that we can more easily assist

Thus we can _quickly_ look at your data, and see if something went
wrong... and you can post as many questions as you need ;-)

Then concerning the match between your FF library (mol2/mol3 FF lib
file) generated by PyRED and your PDB file (macromolecular system with
a ligand?) all the atoms of the ligands are obviously required in the
FF lib.
On the contrary in the PDB file:
- all/some hydrogen and some heavy atoms CAN be missing in the PDB file
- the atom and residue names in the PDB file for the atoms (which are
present) must bear the exact SAME name than in the FF lib.
- other atoms or wrong names in the PDB file leads to mismatch between
the FF lib and pdb files...

    then LEaP will do the job...

regards, Francois

> 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

           F.-Y. Dupradeau

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Received on Thu Jan 26 2017 - 23:00:03 PST
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