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

[Justin Lemkul]

On 11/22/17 9:32 PM, MD wrote:
> ​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.
>
> Ming
>
> [ 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
You need a bond between SG and OE.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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