[gmx-users] error of missing atoms due to an incorrectness in the .hdb file
Lalehan Ozalp
lalehan.ozalp at gmail.com
Sun May 26 15:13:19 CEST 2019
Thank you Justin, I worked more on the format of hydrogen names and I don't
see those errors anymore.
However, the only error I now see is: "Atom H5'1 not found in rtp database
in residue FAD, it looks a bit like H01".
Which is weird, because there is no atom named H5'1 anywhere! Not in the
pdb, not in the rtp, not itp nor hdb file.
This is absolutely a black box to me.
Thanks again!
On Thu, May 23, 2019 at 12:07 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/22/19 4:14 PM, Lalehan Ozalp wrote:
> > Hello all,
> >
> > I am trying to run a simulation with a protein involving a covalently
> bound
> > FAD cofactor. I followed the steps provided on the website
> >
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> > and -I think- added the hydrogens in the .hdb file accordingly. While
> doing
> > this, I specifically used the atom types that gromacs would recognize (I
> > also added relevant .rtp and .itp file to the forcefield in the current
> > working directory).
> >
> > However, several warnings and subsequently a fatal error occurs when I
> run
> > pdb2gmx. I don't prefer using -missing option in this case as it'll
> > probably give a wrong topology.
> >
> > How to come around this? Any help would be appreciated. I provide the
> > warnings and the error message below; as well as the constitution of the
> > hydrogens in the .hdb file:
> > (.hdb file)
> > FAD 6
> > 2 3 H N2 CA NC
> > 3 4 HC CT CA CA
> > 1 1 HC CA CA CT
> > 1 1 H5 CQ NC CA
> > 1 1 H5 CQ NA CT
> > 1 1 HA CA CA CT
> >
>
> This entry cannot be correct, because the same atoms are defined in
> multiple ways. Note that the .hdb file requires atom *names*, not types.
> The errors listed below indicated you have 30 more hydrogens that are
> unaccounted for. FAD is a big molecule, you have to include all the
> hydrogens in the isoalloxazine, adenosine, and ribitol.
>
> -Justin
>
> > WARNING: atom H01 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H01 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H02 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H02 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H03 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H03 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H04H is missing in residue FAD 600 in the pdb file
> > You might need to add atom H04H to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H05 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H05 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H06H is missing in residue FAD 600 in the pdb file
> > You might need to add atom H06H to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H07 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H07 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H08H is missing in residue FAD 600 in the pdb file
> > You might need to add atom H08H to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H09 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H09 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H10 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H10 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H11 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H11 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H12 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H12 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H13 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H13 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H14 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H14 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H15 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H15 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H16 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H16 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H17 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H17 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H18 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H18 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H19 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H19 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H21 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H21 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H22 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H22 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H23 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H23 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H24 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H24 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H25 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H25 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H26 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H26 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H27 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H27 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H29 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H29 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H30 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H30 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H31 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H31 to the hydrogen database of
> > building block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > WARNING: atom H4 is missing in residue FAD 600 in the pdb file
> > You might need to add atom H4 to the hydrogen database of
> building
> > block FAD
> > in the file FAD.hdb (see the manual)
> >
> >
> > -------------------------------------------------------
> > Program: gmx pdb2gmx, version 2016.4
> > Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1584)
> >
> > Fatal error:
> > There were 30 missing atoms in molecule Non-Protein_chain_A2, if you
> want to
> > use this incomplete topology anyhow, use the option -missing
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
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