Glu not found in the rtp entry

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1

GROMACS version: 2019
GROMACS modification: Yes/No
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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 …

2

Hi tarzan,

the last peace of the error message gives already quite some hints:

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
3

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…?

4

Is it that charged terminal amino acids have to be handled differently …?

5

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

6

Hi tarzan,

Thanks for the feedback - nice that you solved the issues, before I could even answer…