Gromacs Fatal Error? Help?

GROMACS version: 2021
GROMACS modification: No
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“Fatal error:
The residues in the chain GDP201–MG202 do not have a consistent type. The
first residue has type ‘Other’, while residue MG202 is of type ‘Ion’. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate
molecule.”

I have multiple questions based on these fatal errors…

I have used spdv to help modify and correct the protein. Are there alternative/trustwrothy programs I can use, how do I troubleshoot these fatal errors?

Based on the fatal error I posted before, how do I fix this?

I am looking to do multiple protein-protein interactions and I am not sure how to go about these fatal errors. I just want to start simulations.

Put a chain terminator line (TER) between different species. pdb2gmx is checking to make sure you don’t have some weird hybrid of a molecule somewhere.

How do you do that?

What would I do if i am docking two proteins or ligand to protein then?

Add a TER line in the PDB file after each chain that is a different species.

(all protein lines)
TER
(all GDP lines)
TER
(MG line)

etc.

Same thing. If it’s a new chemical species, add TER between them.

Now I got this error:

Fatal error:
Residue 1 named MET of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

I corrected the last fatal error. Now I am getting this:

Fatal error:
Residue ‘GDP’ not found in residue topology database

https://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database

I read through it, but it’s not clear how I can include the GDP. Here is what it looks like.

TER

   
HETATM 2661  PA  GDP  201       0.584 -10.787  41.924  1.00 11.70           P  
HETATM 2662  PB  GDP  201       0.810 -12.790  43.990  1.00 10.29           P  
HETATM 2663  C5' GDP  201       3.031 -10.300  41.075  1.00 13.04           C  
HETATM 2664  O5' GDP  201       1.643 -10.514  40.766  1.00 11.87           O  
HETATM 2665  C4' GDP  201       3.658  -9.452  39.972  1.00 14.95           C  
HETATM 2666  O4' GDP  201       3.635 -10.166  38.733  1.00 13.87           O  
HETATM 2667  C3' GDP  201       2.862  -8.207  39.721  1.00 18.31           C  
HETATM 2668  O3' GDP  201       3.763  -7.146  39.359  1.00 21.46           O  
HETATM 2669  C2' GDP  201       1.940  -8.509  38.573  1.00 17.09           C  
HETATM 2670  O2' GDP  201       1.708  -7.389  37.715  1.00 18.59           O  
HETATM 2671  C1' GDP  201       2.822  -9.447  37.800  1.00 13.69           C  
HETATM 2672  N1  GDP  201       2.230 -11.677  33.213  1.00 12.68           N  
HETATM 2673  O1A GDP  201      -0.706 -11.072  41.290  1.00 12.01           O1-
HETATM 2674  O1B GDP  201      -0.631 -12.428  44.292  1.00 10.11           O  
HETATM 2675  C2  GDP  201       2.946 -10.596  33.534  1.00 12.70           C  
HETATM 2676  N2  GDP  201       3.633  -9.932  32.577  1.00 15.51           N  
HETATM 2677  O2A GDP  201       0.664  -9.643  42.908  1.00 13.35           O  
HETATM 2678  O2B GDP  201       0.993 -14.249  43.675  1.00 10.45           O1-
HETATM 2679  N3  GDP  201       2.995 -10.079  34.749  1.00 14.94           N  
HETATM 2680  O3A GDP  201       1.202 -12.088  42.589  1.00 10.62           O  
HETATM 2681  O3B GDP  201       1.791 -12.294  45.043  1.00 10.47           O  
HETATM 2682  C4  GDP  201       2.277 -10.742  35.699  1.00 13.00           C  
HETATM 2683  C5  GDP  201       1.478 -11.934  35.413  1.00 11.75           C  
HETATM 2684  C6  GDP  201       1.497 -12.420  34.062  1.00 11.57           C  
HETATM 2685  O6  GDP  201       0.913 -13.443  33.692  1.00 11.56           O  
HETATM 2686  N7  GDP  201       0.905 -12.325  36.573  1.00 11.96           N  
HETATM 2687  C8  GDP  201       1.318 -11.456  37.512  1.00 13.97           C  
HETATM 2688  N9  GDP  201       2.143 -10.502  36.995  1.00 13.02           N  
HETATM 2689  HN1 GDP  201       2.254 -11.981  32.219  1.00 15.22           H  
HETATM 2690 HN21 GDP  201       4.176  -9.116  32.819  1.00 18.61           H  
HETATM 2691 HN22 GDP  201       3.630 -10.272  31.626  1.00 18.61           H  
HETATM 2692 HO2' GDP  201       1.192  -6.722  38.188  1.00 22.31           H  
HETATM 2693  H8  GDP  201       1.045 -11.519  38.558  1.00 16.77           H  
HETATM 2694  H1' GDP  201       3.467  -8.847  37.143  1.00 16.43           H  
HETATM 2695  H2' GDP  201       1.017  -9.004  38.905  1.00 20.51           H  
HETATM 2696  H3' GDP  201       2.278  -7.947  40.615  1.00 21.97           H  
HETATM 2697  H4' GDP  201       4.687  -9.183  40.249  1.00 17.94           H

TER
  
HETATM 2698 MG    MG  202      -1.549 -11.498  45.876  1.00  9.28          Mg  
CONECT 2661 2664 2673 2677 2680
CONECT 2662 2674 2678 2680 2681
CONECT 2663 2665 2664
CONECT 2664 2661 2663
CONECT 2665 2663 2666 2667 2697
CONECT 2666 2665 2671
CONECT 2667 2665 2668 2669 2696
CONECT 2668 2667
CONECT 2669 2667 2670 2671 2695
CONECT 2670 2669 2692
CONECT 2671 2666 2669 2688 2694
CONECT 2672 2675 2689 2684
CONECT 2673 2661
CONECT 2674 2662
CONECT 2675 2672 2676 2679
CONECT 2676 2675 2690 2691
CONECT 2677 2661
CONECT 2678 2662
CONECT 2679 2675 2682
CONECT 2680 2662 2661
CONECT 2681 2662
CONECT 2682 2679 2683 2688
CONECT 2683 2682 2684 2686
CONECT 2684 2683 2672 2685
CONECT 2685 2684
CONECT 2686 2683 2687
CONECT 2687 2686 2693 2688
CONECT 2688 2671 2682 2687
CONECT 2689 2672
CONECT 2690 2676
CONECT 2691 2676
CONECT 2692 2670
CONECT 2693 2687
CONECT 2694 2671
CONECT 2695 2669
CONECT 2696 2667
CONECT 2697 2665
END

GDP isn’t a part of any of the force fields in GROMACS. You’ll have to construct an .rtp entry yourself (e.g. derived from something present already like ATP by swapping the base and truncating the triphosphate) so you can use pdb2gmx or parametrize it via other means (outside of pdb2gmx).

Now I am running into a new issue… I am so close to getting the simulation done! Few questions. The most urgent one is this:

ERROR 1 [file DRGGMX.ITP, line 8]:
Atomtype O not found

I am trying to use a .mdp file. my ligand ITP file as stated above does have the atomtype oxygen. Here are some of the input files

Ligand ITP:
[ moleculetype ]
; Name nrexcl
GDP 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 O 1 GDP O6 1 -0.239 15.9994
2 C 1 GDP C6 1 0.254 12.0110
3 NR 1 GDP N1 1 -0.002 14.0067
4 H 1 GDP H1 1 -0.013 1.0080

topol.top file:

; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”

#include “DRGGMX.ITP”

; Include water topology
#include “oplsaa.ff/spc.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “oplsaa.ff/ions.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion 1
GDP 1
SOL 9178
SOL 9178
SOL 9178
SOL 9178

And here is my protein.gro file which includes the ligand. And I changed the total number of atoms.

169LYS HZ2 2681 2.358 1.500 3.909
169LYS HZ3 2682 2.504 1.436 3.940
169LYS C 2683 2.176 1.379 3.512
169LYS O1 2684 2.221 1.326 3.613
169LYS O2 2685 2.233 1.256 3.526
202MG MG 2686 3.662 4.445 3.759
1GDP O6 2687 3.908 4.251 2.540
1GDP C6 2688 3.967 4.353 2.577
1GDP N1 2689 4.040 4.427 2.492
1GDP H1 2690 4.041 4.399 2.396
1GDP C2 2691 4.112 4.535 2.524
1GDP N2 2692 4.180 4.602 2.429
1GDP H22 2693 4.231 4.685 2.452
1GDP H21 2694 4.181 4.568 2.335
1GDP N3 2695 4.116 4.587 2.646

My next question is, I tried choosing the parameters. I read up online but I don’t understand some of them. How do I go about choosing?

Also here is my ions.mdp file. I just copied and pasted from online just to see if it works.

;define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 1000 ; 2 * 1000 = 2 ps (should be 50000: 100 ps)
dt = 0.002 ; 2 fs
; Output control
nstxout-compressed = 2 ; save compressed coordinates every 20 fs
nstxout = 0 ; save coordinates
nstvout = 0 ; save velocities
nstenergy = 10 ; save energies every 20 fs
nstlog = 10 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbour searching
ns_type = grid ; search neighbouring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

sorry, for some reason this did not send…

Now I am running into a new issue… I am so close to getting the simulation done! Few questions. The most urgent one is this:

ERROR 1 [file DRGGMX.ITP, line 8]:
Atomtype O not found

I am trying to use a .mdp file. my ligand ITP file as stated above does have the atomtype oxygen. Here are some of the input files

Ligand ITP:
[ moleculetype ]
; Name nrexcl
GDP 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 O 1 GDP O6 1 -0.239 15.9994
2 C 1 GDP C6 1 0.254 12.0110
3 NR 1 GDP N1 1 -0.002 14.0067
4 H 1 GDP H1 1 -0.013 1.0080

topol.top file:

; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”

#include “DRGGMX.ITP”

; Include water topology
#include “oplsaa.ff/spc.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “oplsaa.ff/ions.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion 1
GDP 1
SOL 9178
SOL 9178
SOL 9178
SOL 9178

And here is my protein.gro file which includes the ligand. And I changed the total number of atoms.

169LYS HZ2 2681 2.358 1.500 3.909
169LYS HZ3 2682 2.504 1.436 3.940
169LYS C 2683 2.176 1.379 3.512
169LYS O1 2684 2.221 1.326 3.613
169LYS O2 2685 2.233 1.256 3.526
202MG MG 2686 3.662 4.445 3.759
1GDP O6 2687 3.908 4.251 2.540
1GDP C6 2688 3.967 4.353 2.577
1GDP N1 2689 4.040 4.427 2.492
1GDP H1 2690 4.041 4.399 2.396
1GDP C2 2691 4.112 4.535 2.524
1GDP N2 2692 4.180 4.602 2.429
1GDP H22 2693 4.231 4.685 2.452
1GDP H21 2694 4.181 4.568 2.335
1GDP N3 2695 4.116 4.587 2.646

My next question is, I tried choosing the parameters. I read up online but I don’t understand some of them. How do I go about choosing?

It appears you are using a PRODRG topology for GDP in conjunction with OPLS-AA for the protein. Don’t do this. Not only are the force fields incompatible, but PRODRG topologies are notoriously terrible. They should never be used for MD.

How do you change the topologies?

What do you mean by “change?” You need to generate a topology that is consistent with the parent force field. If you’ve chosen OPLS-AA, you need to use the LigParGen server to generate the ligand topology, for example.

Fatal error:
Atom CG in residue VAL 3 was not found in rtp entry VAL with 16 atoms
while sorting atoms.

Hi, I`ve also some kinda issue with .rtp file, can you help me please?