GROMACS version:
GROMACS modification: No
Hi
Im trying to follow the steps in the article “Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK”. In the article Im trying to create 30 different structures of a peptide using MD for future docking.
I am stuck on the stage of creating the topology file. I did it the way it says in the article- built the peptide using build_seq.py in pymol, caped the C and N (ACE and NME) terminus and the continue to making topology, box, etc.
The command I used is:
gmx_mpi pdb2gmx -f beta_peptide.pdb -o beta_peptide.gro -ignh -ff amber99sb-ildn -water tip3p
and the error (the topolgy file that is created is very short without the structure) is:
Making cmap torsions…
There are 297 dihedrals, 21 impropers, 184 angles
262 pairs, 103 bonds and 0 virtual sites
Total mass 812.778 a.m.u.
Total charge -3.000 e
Writing topology
Back Off! I just backed up posre_Protein.itp to ./#posre_Protein.itp.3#
Processing chain 2 (2 atoms, 1 residues)
Identified residue NME9 as a starting terminus.
Identified residue NME9 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Program: gmx pdb2gmx, version 2023.1
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1064)
Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).
what does this mean? how can I fix this?
Thx
Miriam
In general, with capping groups like ACE and NME, you need to interactively select terminal patching with -ter so that default patches like NH3+ and COO- are not applied. Moreover:
Something seems quite wrong with the chain definition. No sensible protein chain has only two atoms.
Thank you
I fixed the error by changing the pdb file (I saw it had a TER between the last residue and NME) and the topology was written in full length.
But still, when I try to run the command:
gmx_mpi grompp -f vacuum.mdp -c beta_peptide_pbc.gro -p topol.top -o beta_peptide_vac.tpr
how? when I to
gmx_mpi pdb2gmx -f beta.pdb -o beta.gro -ignh -ff amber99sb-ildn -water tip3p this it the topology file
; residue 1 ACE rtp ACE q 0.0
1 CT 1 ACE CH3 1 -0.3662 12.01
2 HC 1 ACE HH31 2 0.1123 1.008
3 HC 1 ACE HH32 3 0.1123 1.008
4 HC 1 ACE HH33 4 0.1123 1.008
5 C 1 ACE C 5 0.5972 12.01
6 O 1 ACE O 6 -0.5679 16 ; qtot 0
; residue 2 PRO rtp PRO q 0.0
7 N 2 PRO N 7 -0.2548 14.01
8 CT 2 PRO CD 8 0.0192 12.01
and the beta.gro is (matches):
1ACE CH3 1 0.067 -0.192 0.306
1ACE HH31 2 -0.019 -0.226 0.267
1ACE HH32 3 0.132 -0.269 0.315
1ACE HH33 4 0.050 -0.153 0.396
1ACE C 5 0.127 -0.087 0.215
1ACE O 6 0.234 -0.032 0.243
2PRO N 7 0.065 -0.055 0.106
2PRO CD 8 -0.060 -0.116 0.067
but when I do gmx_mpi editconf -f beta.pdb -o beta_pbc.gro -bt dodecahedron -d 1.0
the file beta_pbc_gro file is different,
1ACE C 1 3.981 2.524 2.000
1ACE O 2 4.088 2.580 2.028
1ACE CH3 3 3.922 2.419 2.091
1ACE 1HH3 4 3.903 2.461 2.189
1ACE 2HH3 5 3.829 2.382 2.050
1ACE 3HH3 6 3.990 2.336 2.101
2PRO N 7 3.919 2.556 1.891
2PRO CA 8 3.970 2.656 1.799
and when I continue to do:
gmx_mpi editconf -f beta.pdb -o beta_pbc.gro -bt dodecahedron -box 4.852
and then gmx_mpi grompp -f vacuum.mdp -c beta_pbc.gro -p topol.top -o beta_vac.tpr
this error comes up (I sent before, where the names do not mach)
