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

nahren manuel meetnahren at yahoo.com
Fri Mar 13 11:38:00 CET 2009

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
; 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

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
  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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090313/de484e47/attachment.html>

More information about the gromacs.org_gmx-users mailing list