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

MD refmac5 at gmail.com
Sun Nov 26 17:13:37 CET 2017 

​Thank you Justin.

At the mean time I had another error after grompp, "ERROR 1 [file
topol_Protein_chain_E.itp, line 52165]:
  Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

the 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..
I looked at the backbone of the pdb and it looks alright. this error didn't
show up until today when i work from home using gromacs on another server.
DO you think if this is caused by different versions?



On Sun, Nov 26, 2017 at 9:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/17 9:32 AM, MD wrote:
>
>> Thank you Mark.
>>
>> Do you think if the atom types of HE, OE and SG are correct in my
>> merged.rtp? These are the three atoms which have name changing cause of
>> the
>> inserted sulfur. I modified their atom types as well. I need to make sure
>> the type names are correct before I add the bond types in ffbonded.itp.
>>
>
> O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise choice.
> You may also need an entirely different sulfur atom type. Have you assessed
> QM water interactions and dipole moments? Where did these charges come
> from? If you haven't done so already, you need to do some really basic
> validation before attempting to do anything with bonded parameters. The
> dihedrals will be particularly sensitive to the quality of LJ and charge
> terms.
>
> -Justin
>
>
> [ 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
>>     SG    CB
>>     SG    OE
>>      N    HN
>>      N    CA
>>      C    CA
>>      C    +N
>>     CA    HA
>>     CB   HB1
>>     CB   HB2
>>             OE   HE1
>>      O     C
>>
>>
>> On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> You need to specify each bond you want, and for the types of those bonds
>>> to
>>> have parameters available. Bonds are specified with atoms, bond types are
>>> specified with atom types.
>>>
>>> Mark
>>>
>>> On Thu, 23 Nov 2017 04:22 MD <refmac5 at gmail.com> wrote:
>>>
>>> Yes. You are right about the names. I wrote them by memory and they were
>>>> not printed from the terminal. I will try to edit the ffbonded.itp and
>>>>
>>> see
>>>
>>>> how it goes. Thanks!
>>>> Ming
>>>>
>>>> On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>
>>>>
>>>>> On 11/22/17 10:11 PM, MD wrote:
>>>>>
>>>>> ​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
>>>>>>
>>>>>> Make sure you're clear on what needs to be done, because what you've
>>>>> written above is not correct and would never be printed - your dihedral
>>>>>
>>>> is
>>>>
>>>>> a mix of types and names. All parameters are assigned by type, never by
>>>>> name.
>>>>>
>>>>> 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?
>>>>>>
>>>>>> ffbonded.itp
>>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>> 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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>>>>>>>
>>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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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