[gmx-users] Residue not found in topology
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Thu Aug 23 13:52:16 CEST 2018
Hi
You can see that only the problem is coming from hydrogen. So in pdb2gmx
command use -ignh so that it ignores the hydrogen. If you use this this
WARNING will not come.
On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb <zebamir85 at gmail.com> wrote:
> Thanks Justin,
>
> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and
> generated the parameters for KAC.
> The merged.rtp file was modified by adding the KAC parameters
> That issue fixed, but now I'm getting the following warning which
> ultimately results in fatal error.
>
> WARNING: atom HA is missing in residue KAC 33 in the pdb file
> You might need to add atom HA to the hydrogen database of building
> block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HB1 is missing in residue KAC 33 in the pdb file
> You might need to add atom HB1 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HB2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HB2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HG1 is missing in residue KAC 33 in the pdb file
> You might need to add atom HG1 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HG2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HG2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HD1 is missing in residue KAC 33 in the pdb file
> You might need to add atom HD1 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HD2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HD2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HE1 is missing in residue KAC 33 in the pdb file
> You might need to add atom HE1 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HE2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HE2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file
> You might need to add atom HZ1 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HI11 is missing in residue KAC 33 in the pdb file
> You might need to add atom HI11 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HI12 is missing in residue KAC 33 in the pdb file
> You might need to add atom HI12 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HI13 is missing in residue KAC 33 in the pdb file
> You might need to add atom HI13 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HZ2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom HT2 is missing in residue KAC 33 in the pdb file
> You might need to add atom HT2 to the hydrogen database of
> building block KAC
> in the file merged.hdb (see the manual)
>
> How may I fix this issue?
>
> Thanks in advance!
>
>
> On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
> > > Hi
> > > In your tool.top file the particular lys molecule residue name you
> > have
> > > to modify. Then it will work..Actually grompp can't find the molecule
> in
> > > the topology.
> >
> > The error has nothing to do with grompp. The topology was never created
> > because pdb2gmx could not write a topology for KAC.
> >
> > CHARMM36 does support KAC, but not as a standalone residue. In CHARMM,
> > one would generate a normal lysine then patch it with the KAC patch. To
> > make this work in GROMACS, one would have to create a KAC .rtp entry by
> > applying the same logic - modify LYS according to the KAC patch (found
> > in the stream/prot/toppar_all36_prot_modify_res.str file from the
> > tarball distributed by Alex MacKerell:
> > http://mackerell.umaryland.edu/charmm_ff.shtml#charmm).
> >
> > -Justin
> >
> > > On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <
> > 177cy500.bratin at nitk.edu.in>
> > > wrote:
> > >
> > >> Hi
> > >> In your tool.top file the particular lys molecule residue name
> you
> > >> have to modify. Then it will work..Actually grompp can't find the
> > molecule
> > >> in the topology.
> > >>
> > >> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebamir85 at gmail.com> wrote:
> > >>
> > >>> Hi gromacs users,
> > >>>
> > >>> I want to simulate a protein where one of the lysine residues is
> > modified
> > >>> to acetylated lysine and has been denoted by KAC. I want to simulate
> > it by
> > >>> CharmM 36 ff, but it gave me this error.
> > >>>
> > >>>
> > >>> Program gmx pdb2gmx, VERSION 5.1.4
> > >>> Source code file:
> > >>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/
> gmxpreprocess/resall.c,
> > >>> line: 645
> > >>>
> > >>> Fatal error:
> > >>> Residue 'KAC' not found in residue topology database
> > >>> For more information and tips for troubleshooting, please check the
> > >>> GROMACS
> > >>> website at http://www.gromacs.org/Documentation/Errors
> > >>>
> > >>>
> > >>> Is CharmM 36 ff capable to simulate modified residue acetylated
> lysine?
> > >>> If yes, what is the ff compatible notation for acetylated lysine?
> > >>> If not, which ff can I use to simulate acetylated lysine?
> > >>>
> > >>> Thanks in advance!
> > >>>
> > >>> Amir
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
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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.thelemkullab.com
> >
> > ==================================================
> >
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