[gmx-users] Residue not found in topology

Amir Zeb zebamir85 at gmail.com
Thu Aug 23 14:12:38 CEST 2018


Thanks Justin,
I have followed what did you suggest for .rtp entry in merged.rtp file of
charmm36 ff.
But i could not make .hdb file for ALY. Where can i find the H-information
for ALY to insert them in merged.hdb file of charmm36 ff?

Amir

On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/23/18 7:52 AM, Bratin Kumar Das wrote:
> > 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.
>
> That's not true. The -ignh option ignores H atoms in the input
> coordinate file and is useful when there are H atoms with names that do
> not agree with what is specified in the .rtp entry for the given
> residue. The OP's problem is the opposite: the H are not there but need
> to be built.
>
> -Justin
>
> > 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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> >> or
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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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> --
> ==================================================
>
> 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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