# Glu not found in the rtp entry
**URL:** https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005
**Category:** User discussions
**Created:** [October 26, 2020, 7:53am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005 "2020-10-26T07:53:23Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@tarzan](https://gromacs.bioexcel.eu/u/tarzan)
#### Post date: [October 26, 2020, 7:53am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/1 "2020-10-26T07:53:23Z")
GROMACS version: 2019
GROMACS modification: Yes/No
Here post your question
Hi all
After docking a ligand with a protein, I am using the generated pose for MD simulations using GROMACS
I end up with this error for the topology generation of the protein
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 85 residues with 1210 atoms
chain #res #atoms
1 ‘A’ 85 1210
All occupancies are one
Opening force field file ./charmm36-jul2020.ff/atomtypes.atp
Atomtype 448
Reading residue database… (Charmm36-jul2020)
Opening force field file ./charmm36-jul2020.ff/merged.rtp
Residue 1248
Sorting it all out…
Opening force field file ./charmm36-jul2020.ff/merged.hdb
Opening force field file ./charmm36-jul2020.ff/merged.n.tdb
Opening force field file ./charmm36-jul2020.ff/merged.c.tdb
Processing chain 1 ‘A’ (1210 atoms, 85 residues)
Identified residue GLU2 as a starting terminus.
Identified residue GLN86 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET21
SD268
MET75 SD1033 0.514
Start terminus GLU-2: NH3+
End terminus GLN-86: COO-
Opening force field file ./charmm36-jul2020.ff/merged.arn
* * *
Program: gmx pdb2gmx, version 2019
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)
Fatal error:
Atom HB3 in residue GLU 2 was not found in rtp entry GLU with 17 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
Pls let me know what needs to be done …
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### Author:  [@cblau](https://gromacs.bioexcel.eu/u/cblau)
#### Post date: [October 26, 2020, 10:52am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/2 "2020-10-26T10:52:57Z")
Hi tarzan,
the last peace of the error message gives already quite some hints:
> [@tarzan](#):
>
> For a hydrogen, this can be a different protonation state, or it
> might have had a different number in the PDB file and was rebuilt
> (it might for instance have been H3, and we only expected H1 & H2).
> Note that hydrogens might have been added to the entry for the N-terminus.
> Remove this hydrogen or choose a different protonation state to solve it.
> Option -ignh will ignore all hydrogens in the input.
So, the following scenarios might apply:
- You have another protonation state, so you would like to name your residue different accordingly ( in this case it might be `GLH`)
- hydrogen atoms have received names that gromacs does not understand in your .pdb file due to some pre-processing, using `-ignh` might help, but beware of protonation states - if you use that option, you’ll never discover if you missed out on protonation state information
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### Author:  [@tarzan](https://gromacs.bioexcel.eu/u/tarzan)
#### Post date: [October 27, 2020, 6:34am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/3 "2020-10-27T06:34:09Z")
Hi,
Actually I have preprossed the .pdb file which I got from RCSB using Schrodinger. It has a net charge of -4. Should the protein be neutral for generating the topology…?
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### Author:  [@tarzan](https://gromacs.bioexcel.eu/u/tarzan)
#### Post date: [October 27, 2020, 8:11am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/4 "2020-10-27T08:11:55Z")
Is it that charged terminal amino acids have to be handled differently …?
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### Author:  [@tarzan](https://gromacs.bioexcel.eu/u/tarzan)
#### Post date: [October 27, 2020, 10:24am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/5 "2020-10-27T10:24:42Z")
Dear All
I have used CHARMM-GUI and uploaded my file which converted in into CHARMM compatible format and topology was successfully generated using CHARMM FF…
Thank you @cblau once again
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### Author:  [@cblau](https://gromacs.bioexcel.eu/u/cblau)
#### Post date: [October 27, 2020, 11:10am UTC](https://gromacs.bioexcel.eu/t/glu-not-found-in-the-rtp-entry/1005/6 "2020-10-27T11:10:00Z")
Hi tarzan,
Thanks for the feedback - nice that you solved the issues, before I could even answer…