GROMACS version: 2020
GROMACS modification: Yes/No
Here post your question I have been attempting to do a Protein-Ligand simulation and ran into an error. I converted the pdb file of the protein to generate a .gro file, a itp (posre) file, and a topol.top file. I used LigParGen to create the .itp and .gro file for the ligand. When I attempted to structure the topol.top file to include the Ligands files I ran into an error when trying to add ions to the box. The error read as follows
ERROR 1 [file topol.top, line 28656]:
Atomtype opls_800 not found
There was 1 note
Program: gmx grompp, version 2020
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1408)
The following is the line noted in the error (28656). Additionally I am adding a few lines above the errored line. That was where I added the Posre file for the Protein. The line which was flagged for the error is the list line below.
; Include Position restraint file #ifdef POSRES1 #include “posre.itp” #endif
[ moleculetype ]
; Name nrexcl
GTP 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 UNK P00 1 2.7088 30.9738
It appears to be an error with the residue identification. I used LigParGen’s OPLS/CM1A Parameter Generator for Organic Ligands to get the ligand but I keep on getting this error. Do you know why I am running into this error and what I can do to fix it?
When you generated the .itp file, there should be a section labeled atomtypes defining each atom that needs to be called before any residues are defined. You can call them with the #include command, make sure they appear before any moleculetypes are defined
what do you mean by call? Should I rename them?
This is what my atomtype looks like now-
[ atomtypes ]
opls_808 O808 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_823 N823 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_825 N825 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_832 H832 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_806 O806 15.9990 0.000 A 2.90000E-01 5.85760E-01
After that comes the molecule type which reads as follows-
[ moleculetype ]
; Name nrexcl
GTP 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 UNK P00 1 2.7088 30.9738
2 opls_801 1 UNK O01 1 -1.1224 15.9990
3 opls_802 1 UNK O02 1 -0.9331 15.9990
4 opls_803 1 UNK H03 1 0.4396 1.0080
5 opls_804 1 UNK O04 1 -0.8933 15.9990
6 opls_805 1 UNK H05 1 0.4334 1.0080
It appears that the issue is with the lack of residue names and type. How do I generate the names for the residues and the atom type so that gromacs can recognize it?
By call, I mean the topol.top file will use the parameters provided by the .itp files through the #include command. The [ atomtypes ] defines the atoms and the [ moleculetype ] and [ atoms ] uses those atoms to define whatever residue you’re working with. All [ atomtypes ] must be included (either in an .itp file or in topol.top itself) before any residues can be defined.
Was the water topology included before or after your [atomtypes] (should look something like #include ‘…/tip3p’, or whichever water model you’re using)? Could you make sure that the [atomtypes] is included before the water topology is called (the water topology file likely includes a [ moleculetype ] section for the water model, so you need to make sure your [ atomtypes ] are listed before the water model), and also make sure UNK is listed as GTP or vice versa (just so the residue name under [moleculetype] and [atoms] match)?
Hello all,
I am new to Gromacs. I ran MD simulation for apo protein successfully. But I am facing a lot of issues while running simulation for protein-ligand complex. I have installed the gromacs 2023 version and chramm force field 2022 version. While applying the terminus type, I am getting fatal error for C-terminus type. Any suggestions and help will be highly appreciated. Thank you in advance.
Hello, could you post the exact command you used and copy-paste all the messages that were output into the terminal/output file when you ran the command (so all the notes, warnings and error messages)? Also, could you make a new post for this, just so this one post doesn’t get cluttered with unrelated replies?