[gmx-users] pdb2gmx assign CSER to non-terminal serine

[Zheng Ruan]

Hi Gromacs Users,

I'm using pdb2gmx to process my pdb files with a phospho-tyrosine
using amber99sb-ildn.ff. The relavant content in my pdb looks like this
(There is a serine before phosphorylated tyrosine):

ATOM    202  N   SER    26      31.593 -68.669 -25.834  1.00208.96
  N
ATOM    203  CA  SER    26      32.638 -67.843 -25.302  1.00208.96
  C
ATOM    204  C   SER    26      31.995 -66.621 -24.727  1.00208.96
  C
ATOM    205  O   SER    26      30.979 -66.149 -25.232  1.00208.96
  O
ATOM    206  CB  SER    26      33.644 -67.365 -26.363  1.00208.96
  C
ATOM    207  OG  SER    26      34.330 -68.476 -26.921  1.00208.96
  O
ATOM    208  N   Y2P    27      32.567 -66.088 -23.628  1.00307.13
  N
ATOM    209  CA  Y2P    27      32.019 -64.903 -23.034  1.00307.13
  C
ATOM    210  C   Y2P    27      33.156 -64.013 -22.644  1.00307.13
  C
ATOM    211  O   Y2P    27      34.263 -64.481 -22.390  1.00307.13
  O
ATOM    212  CB  Y2P    27      31.197 -65.174 -21.762  1.00307.13
  C
ATOM    213  CG  Y2P    27      30.697 -63.861 -21.266  1.00307.13
  C
ATOM    214  OG  Y2P    27      29.295 -60.184 -19.874  1.00307.13
  O
ATOM    215  CD1 Y2P    27      29.578 -63.285 -21.820  1.00307.13
  C
ATOM    216  CD2 Y2P    27      31.346 -63.208 -20.242  1.00307.13
  C
ATOM    217  CE1 Y2P    27      29.115 -62.073 -21.365  1.00307.13
  C
ATOM    218  CE2 Y2P    27      30.887 -61.996 -19.783  1.00307.13
  C
ATOM    219  CZ  Y2P    27      29.768 -61.428 -20.343  1.00307.13
  C
ATOM    220  P   Y2P    27      29.208 -59.251 -20.980  0.00  0.00
  P
ATOM    221  O1P Y2P    27      30.631 -58.900 -21.344  0.00  0.00
  O
ATOM    222  O2P Y2P    27      28.565 -59.705 -22.398  0.00  0.00
  O
ATOM    223  O3P Y2P    27      28.289 -58.144 -20.524  0.00  0.00
  O

I followed the online protocol to convert the amber parameters from Bryce
into my force field. The Y2P entry in aminoacids.rtp I add looks like this:

[ Y2P ]
 [ atoms ]
     N    N           -0.516300     1
     H    H            0.293600     2
    CA    CT           0.141279     3
    HA    H1           0.027982     4
    CB    CT          -0.251171     5
   HB1    HC           0.081930     6
   HB2    HC           0.081930     7
    CG    CA           0.073446     8
   CD1    CA          -0.198084     9
   HD1    HA           0.112503    10
   CE1    CA          -0.254266    11
   HE1    HA           0.161606    12
    CZ    C            0.477009    13
   CE2    CA          -0.254266    14
   HE2    HA           0.161606    15
   CD2    CA          -0.198084    16
   HD2    HA           0.112503    17
    OG    OS          -0.557944    18
     P    P            1.380672    19
   O1P    O2          -0.943550    20
   O2P    O2          -0.943550    21
   O3P    O2          -0.943550    22
     C    C            0.536600    23
     O    O           -0.581900    24
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   CD1
    CG   CD2
   CD1   HD1
   CD1   CE1
   CE1   HE1
   CE1    CZ
    CZ    OG
    CZ   CE2
   CE2   HE2
   CE2   CD2
   CD2   HD2
    OG   P
     P   O1P
     P   O2P
     C     O
    -C     N
 [ impropers ]
    -C    CA     N     H
    CA    +N     C     O
    CG   CE2   CD2   HD2
    CZ   CD2   CE2   HE2
   CD1    CZ   CE1   HE1
    CG   CE1   CD1   HD1
   CD1   CD2    CG    CB
   CE1   CE2    CZ    OG

I also modified the aminoacids.hdb and ffbonded.itp accordingly. I then use
the following command to process the pdb file:

# g_pdb2gmx -f file.pdb -o file.gro -ignh
...
Changing rtp entry of residue 26 SER to 'CSER'
...
Renaming atom 'O' in residue 26 SER to 'OC2'
...

The seine before Y2P is changed to CSER, which is the terminal version of
serine. This creates trouble for further steps to prepare my MD. Is this
because I have a mistake in defining Y2P entry? Can I force pdb2gmx not
chaning SER26 to CSER? I can provide additional information if needed.
Thank you!

Best,
Ruan