[gmx-users] pdb2gmx fatal error
Ali Khodayari
ali.khodayari at student.kuleuven.be
Thu Nov 8 19:37:21 CET 2018
Dear Justin,
Thank you for your response. Yet, I have not been able to solve the problem.
The structure looks fine but gromacs is complaining about a dangling atom at
one of the terminal ends, if I choose no terminal to be added. While,
assigning a terminal to the ends (which I don't understand why), results to
another error, which to me seems bizarre. It is still complaining about an
atom (C6) which is not found in the input file (.rtp?), however, it is
indeed one of the atoms in the rtp file.
Here is what it looks like in the rtp file:
[ GLC0 ]
[ atoms ]
C4 CH1R 0.23200 1
O4 OA -0.64200 1
HO4 H 0.41000 1
C3 CH1R 0.23200 2
O3 OA -0.64200 2
HO3 H 0.41000 2
C2 CH1R 0.23200 3
O2 OA -0.64200 3
HO2 H 0.41000 3
C6 CH2 0.23200 4
O6 OA -0.64200 4
HO6 H 0.41000 4
C5 CH1R 0.23200 0
O5 OR -0.46400 0
C1 CH1R 0.46400 0
O1 OE -0.46400 0
And the pdb input file is:
ATOM 1 C1 GLC0 1 3.992 3.199 3.177 1.00 0.04
C
ATOM 2 C2 GLC0 1 3.597 2.204 2.072 1.00 0.04
C
ATOM 3 C3 GLC0 1 4.231 2.633 0.737 1.00 0.04
C
ATOM 4 C4 GLC0 1 3.713 4.036 0.378 1.00 0.04
C
ATOM 5 C5 GLC0 1 4.096 5.017 1.502 1.00 0.04
C
ATOM 6 C6 GLC0 1 3.581 6.419 1.132 1.00 0.04
C
ATOM 7 O2 GLC0 1 4.094 0.828 2.442 1.00 0.04
O
ATOM 8 O5 GLC0 1 3.476 4.569 2.805 1.00 0.04
O
ATOM 9 O6 GLC0 1 4.207 6.834 -0.178 1.00 0.04
O
ATOM 10 H1 GLC0 1 5.128 3.219 3.268 1.00 0.00
H
ATOM 11 H2 GLC0 1 2.462 2.181 1.967 1.00 0.00
H
ATOM 12 H3 GLC0 1 5.366 2.661 0.847 1.00 0.00
H
ATOM 13 H4 GLC0 1 2.578 4.005 0.271 1.00 0.00
H
ATOM 14 H5 GLC0 1 5.230 5.045 1.611 1.00 0.00
H
ATOM 15 H61 GLC0 1 3.858 7.165 1.950 1.00 0.00
H
ATOM 16 H62 GLC0 1 2.449 6.385 1.015 1.00 0.00
H
ATOM 17 HO2 GLC0 1 5.198 0.853 2.551 1.00 0.00
H
ATOM 18 HO6 GLC0 1 5.313 6.850 -0.083 1.00 0.00
H
ATOM 19 O4 GLC0 2 4.312 4.595 9.824 1.00 0.04
O
ATOM 20 C1 GLC0 2 3.708 4.145 8.515 1.00 0.04
C
ATOM 21 C2 GLC0 2 4.109 5.126 7.399 1.00 0.04
C
ATOM 22 C3 GLC0 2 3.497 4.668 6.062 1.00 0.04
C
ATOM 23 C4 GLC0 2 4.005 3.250 5.730 1.00 0.04
C
ATOM 24 C5 GLC0 2 3.616 2.295 6.877 1.00 0.04
C
ATOM 25 C6 GLC0 2 4.151 0.877 6.596 1.00 0.04
C
ATOM 26 O2 GLC0 2 3.601 6.506 7.743 1.00 0.04
O
ATOM 27 O3 GLC0 2 3.909 5.661 5.002 1.00 0.04
O
ATOM 28 HO4 GLC0 2 4.850 3.729 10.263 1.00 0.00
H
ATOM 29 O1 GLC0 1 3.396 2.685 4.467 1.00 0.04
O
ATOM 30 O5 GLC0 2 4.225 2.770 8.173 1.00 0.04
O
ATOM 31 O6 GLC0 2 3.558 0.309 5.328 1.00 0.04
O
ATOM 32 H1 GLC0 2 2.572 4.115 8.609 1.00 0.00
H
ATOM 33 H2 GLC0 2 5.244 5.151 7.307 1.00 0.00
H
ATOM 34 H3 GLC0 2 2.361 4.651 6.153 1.00 0.00
H
ATOM 35 H4 GLC0 2 5.141 3.258 5.636 1.00 0.00
H
ATOM 36 H5 GLC0 2 2.480 2.262 6.979 1.00 0.00
H
ATOM 37 H61 GLC0 2 3.879 0.196 7.468 1.00 0.00
H
ATOM 38 H62 GLC0 2 5.286 0.920 6.494 1.00 0.00
H
ATOM 39 HO2 GLC0 2 2.496 6.480 7.836 1.00 0.00
H
ATOM 40 HO3 GLC0 2 5.015 5.674 4.919 1.00 0.00
H
ATOM 41 HO6 GLC0 2 2.453 0.270 5.418 1.00 0.00
H
ATOM 42 O3 GLC0 1 3.852 1.653 -0.348 1.00 0.00
O
ATOM 43 HO3 GLC0 1 4.305 1.969 -1.311 1.00 0.00
H
END
The error is given as a result of the command: gmx pdb2gmx -f
cellobiose.pdb -o cellobiose.gro -ignh -ter
The error:
Fatal error:
Residue 4 named GLC0 of a molecule in the input file was mapped
to an entry in the topology database, but the atom C6 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Do you have any idea why it is happening?
Thank you in advanced.
Regards,
Ali
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Lemkul
Sent: donderdag 8 november 2018 13:57
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pdb2gmx fatal error
On 11/7/18 1:05 PM, Ali Khodayari wrote:
> Dear gmx users,
>
>
>
> I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom
> names were modified according to the rtp file of the force field. Yet,
> I get the following error while I perform pdb2gmx command:
>
>
>
> Fatal error:
>
> Residue 4 named GLC of a molecule in the input file was mapped to an
> entry in the topology database, but the atom C6 used in that entry is
> not found in the input file. Perhaps your atom and/or residue naming needs
to be fixed."
>
>
>
> I also tried to delete the hydrogens in the pdb file but the error
> changed to the following:
>
>
>
> Fatal error:
>
> Residue 876814369 named GLC of a molecule in the input file was mapped
> to an entry in the topology database, but the atom C3 used in an
> interaction of type improper in that entry is not found in the input
> file. Perhaps your atom and/or residue naming needs to be fixed.
>
>
>
> Ignoring the hydrogens through -ignh will give the first error as well.
> Then I added the GLC residue to the residuetypes.dat and the error
> changed
> to:
Your problem is not related to hydrogens. pdb2gmx is complaining about
carbon nomenclature.
http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_
in_rtp_entry
>
>
> Fatal error:
>
> atom N not found in buiding block 1GLC while combining tdb and rtp
>
>
This error comes from letting pdb2gmx apply default protein terminal
patches. For a carbohydrate, you probably should have definitions for
properly constructed reducing and non-reducing ends (e.g. different from
internal residues) and apply no terminal patching.
-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.thelemkullab.com
==================================================
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