[gmx-users] my modified residue falls apart after MD

MD refmac5 at gmail.com
Thu Nov 23 03:32:25 CET 2017

​Hi gromacs folks,

I was trying to introduce sulfenic acid as modified cysteine to the
forcefield as following. Everything went well until the "gmx mdrun -v
-deffnm em". The only file I modified was merged.rtp since there were no
new bond or dihedral angles. However my sulfenic acid falls apart (oxygen
and sulfur are far away from the protein) after mdrun. Any help or
suggestions what I should do next? I am reading the manual at the same time
but I thought maybe I can get some help here as well.

Thank you for your time and any advice will be appreciated.


[ CSO ]
  [ atoms ]
    N   NH1   -0.470  0
   HN     H    0.310  1
   CA   CT1    0.070  2
   HA   HB1    0.090  3
   CB   CT2   -0.110  4
  HB1   HA2    0.090  5
  HB2   HA2    0.090  6
   SG     S    0.6    7
   OE     O   -0.83   8
   HE1    H    0.160  9
    C     C    0.510  10
    O     O   -0.510 11
  [ bonds ]
   CB    CA
   S    CB
   S    O
    N    HN
    N    CA
    C    CA
    C    +N
   CA    HA
   CB   HB1
   CB   HB2
           OE   HE1
    O     C

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