[gmx-users] phosphorylated protein parametrization

[Robert König]

Hi,
you have to implement it in the forcefield you are going to use.I use AMBER03 and AMBER99SB-ILDN
First you need the parameters. 
I took these:http://research.bmh.manchester.ac.uk/bryce/amber

Then you have to follow these instructions:Copy the forcefield and residuetypes.dat to your working directory!Then follow the steps. This is what I added:

1. aminoacids.rtp
[ TPO ] ; Phosphothreonine aus http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.THP.unit.atoms table
     N    N           -0.493700    1
     H    H            0.301800    2
    CA    CT          -0.1740      3
    HA    H1           0.016400    4
    CB    CT           0.15310     5
    HB    H1          -0.090900    6
   CG2    CT          -0.16170     7
  HG21    HC           0.049600    8
  HG22    HC           0.049600    9
  HG23    HC           0.049600   10
   OG1    OS          -0.637500   11
     P    P            1.400      12
   O1P    O2          -0.850      13
   O2P    O2          -0.850      14
   O3P    O2          -0.850      15
     C    C            0.673100   16
     O    O           -0.585400   17
 [ bonds ] ; !entry.THP.unit.connectivity table
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB    HB
    CB   CG2
    CB   OG1
   CG2  HG21
   CG2  HG22
   CG2  HG23
   OG1     P
     P   O1P
     P   O2P
     P   O3P
     C     O
    -C     N   
 [ impropers ] 
    -C    CA     N     H
    CA    +N     C     O


2. aminoacids.hdb
;added 
TPO     4
1       1       H       N       -C      CA
1       5       HA      CA      N       CB      C
1       5       HB      CB      CA      CG2     OG1
3       4       HG2     CG2     CB      CA

3. - no new atom types used

4. - no new bonds used

5. residuetypes.dat
TPO      Protein

6. - no connections added


That is how I implemented it. It works. 
If someone finds something I missed, I would be glad to hear it.
Best Regards.




 

    "zeljko.svedruzic at biotech.uniri.hr" <zeljko.svedruzic at biotech.uniri.hr> schrieb am 18:16 Donnerstag, 7.Dezember 2017:
 

 

Hi folks,
what do I need to do to run pdb2gmx with a protein pdb file that contains
phosphorylated THR labeled as THP? I see several solutions but no of them
look elegant. Does anybody have any experience with this,
Thanks for any advice,
Cheers,
www.svedruziclab.com

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