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

Mark Abraham mark.j.abraham at gmail.com
Thu Nov 23 06:25:33 CET 2017 

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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