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

[MD]

Thanks Justin. Then do I need to create new bond of SG and OE in
ff​bonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp and
I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and
it should work...

On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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