[gmx-users] WG: Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

[Robert König]

Hi,


I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. following the instructions on 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
I added TPO and SEP to aminoacids.rtp like:
[ TPO ] ; Phosphothreonine from 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    PS
     S   O1P
     S   O2P
     S   O3P
     C     O
    -C     N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA     N     H
    CA    +N     C     O

[ SEP ] ; Phosphoserine from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib 
; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
 [ atoms ] ; !entry.SEP.unit.atoms table
     N    N           -0.493700    1
     H    H            0.301800    2
    CA    CT          -0.238000    3
    HA    H1           0.093700    4
    CB    CT           0.078200    5
   HB2    H1          -0.060200    6
   HB3    H1          -0.060200    7
    OG    OS          -0.559300    8
     P    P            1.4         9
   O1P    O2          -0.850      10
   O2P    O2          -0.850      11
   O3P    O2          -0.850      12
     C    C            0.673100   13
     O    O           -0.585400   14
 [ bonds ] ; !entry.THP.unit.connectivity table
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB2
    CB   HB3
    CB    OG
    OG    PS
     S   O1P
     S   O2P
     S   O3P
     C     O
    -C     N   ; is present everywhere else
 [ impropers ] ; is present everywhere else
    -C    CA     N     H
    CA    +N     C     O
My first question is, like I commented, on both entries the last four lines are not in the parameters I got from 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib and 
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.libbut are found on all the other entries.So do I need these lines, are they right that way and what does it mean?

Second is in aminoacid.hdb.The entries look like:
"THR    5"
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    
1    2    HG1    OG1    CB    CA
So I added till now:
TPO     4
1               H
1               HA 
1               HB
3               HG2
SEP     4
1               H
1               HA
1               HB2
1               HB3
is this right that far, especially TPO with 4 lines and 3 HG2?If somebody added these AA already I would be grateful for the missing parameters or a reliable source, I am not sure that my own estimations will be totally right.
Thanks a lot!
If you are still in good mood I would be very glad if you would a quick glance at my whole proceding. It is my first time to add residues and it would be good to know if I missed something or made a mistake.
I followed http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

1. I added the parameter like in my first question.2. See my second question.3. Nothing - I didn't introduce new atom types
4. Nothing - I didn't require new bonded types
5. I added:TPO      Protein
SEP      Proteinto residuetypes.dat6. Nothing - There is new special connectivity to other residues.
So is that everything I have to do and do you see any mistakes?
Thank you very much!Sincerly, olaf