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

[MD]

​Justin, originally I did use SG and OE in the [bond​s] and I got
complaints of "SG-OE no default bond type" "CB SG OE" no default U-B type
and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
parameters you mean that are missing? If so, what files do you think I
should modify to create these parameters? ffbonded.itp, merged.rtp and
residuetype.dat?

On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
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