[gmx-users] sridhar: How to include topologies for unusual/phosphorylated residues occurring within the protein chain.

Paul Barrett barrett at biop.ox.ac.uk
Fri May 16 11:05:01 CEST 2003

Using Grahams force field sounds like a good idea. However if you want
to do it yourself 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...!

Below is the full text for the phosphorylated Threonine from my

Paul Barrett
University of Oxford 
Dept of Biochemistry
barrett at biop.ox.ac.uk

[ TPO ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH1     0.15000     2
  OG1    OA    -0.54800     2
    P     P	0.79800     2
  O1P    OM    -0.80000     2
  O2P    OM    -0.80000     2
  O3P    OM    -0.80000     2
  CG2   CH3     0.00000     3
    C     C       0.380     4
    O     O      -0.380     4
 [ bonds ]
    N     H    gb_2    
    N    CA    gb_20   
   CA     C    gb_26   
    C     O    gb_4    
    C    +N    gb_9    
   CA    CB    gb_26   
   CB   OG1    gb_17   
   CB   CG2    gb_26   
    P   O1P    gb_23   
    P   O2P    gb_23
    P   O3P    gb_23
    P   OG1    gb_27
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31   
    H     N    CA     ga_17   
   -C     N    CA     ga_30   
    N    CA     C     ga_12   
   CA     C    +N     ga_18   
   CA     C     O     ga_29   
    O     C    +N     ga_32   
    N    CA    CB     ga_12   
    C    CA    CB     ga_12   
   CA    CB   OG1     ga_12   
   CA    CB   CG2     ga_14   
  OG1    CB   CG2     ga_14   
  OG1     P   O1P     ga_23
  OG1     P   O2P     ga_23
  OG1     P   O3P     ga_23
   CB   OG1     P     ga_27
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_28
  O2P     P   O3P     ga_28
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1    
    C    CA    +N     O     gi_1    
   CA     N     C    CB     gi_2    
   CB   OG1   CG2    CA     gi_2    
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4    
   -C     N    CA     C     gd_19   
    N    CA     C    +N     gd_20   
    N    CA    CB   OG1     gd_17   

>Dear Gromacs users,
>I am a graduate student at Centre for DNA Fingerprinting and Diagnostics,
>Hyderabad, India. I am currently working on Dynamic simulation studies
>using GROMACS software.
>In my current work I want to do simulation of a protein containing
>PhosphoSerine. Regarding this I went through the Article "Gromacs Tutorial
>for Drug-Enzyme Complex" which has shown clearly step-by-step how to
>include new topologies for drug/ligand molecules.
>By I was not successful in running the dynamics. I got topology for
>Phosphoserine from PRODRG server. The "Drug-Enzyme complex" tutorial was
>specific for ligands/Drugs that do not form part of the protein chain. But
>if I want to include topology for special residues like Phosphoserine
>which occur within the protein chain, how to do it?
>I tried according to the tutorial but was unsuccessful all the time.
>I'll be very grateful if you can outline me the procedure to be
>followed in such cases.
>Thankyou very much.
>On Sat, 10 May 2003, Mr.Sridhar wrote:
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