[gmx-users] how to parametrize Phos. Thr TPO

[Lucio Ricardo Montero Valenzuela]

There is already a user contribution in the gromacs page named ffG43a1p, that is
based in the force field ffG43a1 and also includes phosphorilated serine end
threonine. However, is exciting doing it for yourself.
Mensaje citado por nahren manuel <meetnahren at yahoo.com>:

> Dear Gromacs Users,
>
> I am trying to simulate a protein whose Thr residues is phosphorylated.
> I did the following based on the earlier query regarding the same
> ----
> .... here is how I did it for phosphorylated Threonine.
>
>
> 1) open the appropriate .rtp file e.g. ffG43a1.rtp
> 2) make a copy of the existing entry for the residue
> you want to phosphorylate it.
>
> here are the notes I made as I did it...comments
> welcome if anyone
> doesnt like how I did it!
>
> ; TPO which follows is phosphorylated Threonine and
> was derived thus:
> ; 1) take THR entry
> ; 2) add P, O1P, O2P, O3P atoms
> ; 3) remove HG1 atom
> ; 4) assign partial charges to give an overall
> molecule -2 charge
> ;     with this charge localised on the Phosphate
> group.
> ; 5) add bonds for OG1 to P and the OxPs. took bond
> tpyes from [ DADE ]
> ; 6) likewise took angle types from [ DADE ]
> ; 7) removed final dihedral which contained H1 (had
> considered changing
> it for
> ;     P but dont want to limit Phoshphate group too
> much)
>
> 3) you will need to add the new residue to the file
> aminoacids.dat if
> you want the residue to be recognised as part of the
> protein in
> subsequent analysis. Make sure you increment the count
> on the top line
> of aminoacids.dat. dont put any comments in
> aminoacids.dat becuase it
> has unpredictable effects on results.
> 4) update the hydrogen database entry too if you are
> expecting pdb2gmx
> or protonate to work properly.
>
> I *think* that was it...!
> ....
> Paul Barrett
>
> ----
> but i get the following error
>  * * * * *
> Generated 380 of the 1326 non-bonded parameter combinations
> ERROR 0 [file "top_A.itp", line 16530]:
>   No default Proper Dih. types
> ERROR 0 [file "top_A.itp", line 16531]:
>   No default Proper Dih. types
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> NOTE:
>   System has non-zero total charge: -1.999996e+00
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   5789
> #  G96ANGLES:   8462
> #      PDIHS:   3040
> #      IDIHS:   2893
> #       LJ14:   9248
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1182
>
> Fatal error:
> There were 2 errors in input file(s)
> -------------------------------------------------------
>
> "Ich Bin Ein Berliner" (J.F. Kennedy)
> * * * * * *
>
> Kindly advice
> nahren
>
>
>
>
>
>


Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico

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