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

[Justin Lemkul]

On 11/22/17 9:57 PM, MD wrote:
> 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

SG and OE are atom names, not types. That's not a valid approach.

> I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and
> it should work...

The [bonds] section requires atom names in order to function, so use of 
SG and OE here is correct (your original entry used S and O, which are 
atom types and therefore not correct). If grompp subsequently complains 
about missing force field parameters when the correct bonds are written 
to the topology, then what you're attempting to do is not supported by 
the force field and you will have to either parametrize those missing 
interactions or find parameters.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================