[gmx-users] Residue not found in topology

[Amir Zeb]

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
> >>> --
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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
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>
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