Protein-ligand-simul

User discussions
1

GROMACS version:2020
GROMACS modification: Yes
Here post your question

Hey,
I have been trying to perform protein-ligand simulations. I have a docked complex from the maestro and saved it in a PDB format and now trying to proceed for MD simulation via gromacs.

command : /usr/local/gromacs/gmx pdb2gmx -f test-lig-covdock.pdb -o test.gro

Here’s the error :
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 ‘B’ (2662 atoms, 175 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 278 donors and 260 acceptors were found.
There are 326 hydrogen bonds
Will use HISD for residue 184
Will use HISE for residue 222
Will use HISE for residue 285
Will use HISE for residue 293

Program: gmx pdb2gmx, version 2020
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 902)

Fatal error:
The residues in the chain ACE167–NMA340 do not have a consistent type. The
first residue has type ‘Protein’, while residue NMA340 is of type ‘Other’.
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.

2

Hi Sanah,

There might be a couple of reasons behind this but on first sight it might be that the docked ligand has the same chain ID as the protein. In this case, try changing the chain id of the ligand.

3

My pdb looks like:
TITLE dk23
MODEL 1
ATOM 1 CH3 ACE B 167 -3.289 33.877 3.011 1.00 0.00 C
ATOM 2 C ACE B 167 -4.777 34.143 2.829 1.00 0.00 C
ATOM 3 O ACE B 167 -5.340 33.819 1.785 1.00 0.00 O
ATOM 4 1H ACE B 167 -2.894 33.305 2.170 1.00 0.00 H
ATOM 5 2H ACE B 167 -2.739 34.817 3.071 1.00 0.00 H
ATOM 6 3H ACE B 167 -3.109 33.309 3.925 1.00 0.00 H
ATOM 7 N GLN B 168 -5.409 34.750 3.848 1.00 49.37 N
ATOM 8 CA GLN B 168 -6.843 35.061 3.876 1.00 51.45 C
…
…
ATOM 2656 HG2 PRO B 340 -42.350 26.052 -11.892 1.00 0.00 H
ATOM 2657 N NMA B 340A -45.083 27.778 -11.403 1.00 0.00 N
ATOM 2658 CA NMA B 340A -46.296 27.362 -10.719 1.00 0.00 C
ATOM 2659 H NMA B 340A -44.343 28.170 -10.840 1.00 0.00 H
ATOM 2660 1HA NMA B 340A -46.479 26.297 -10.866 1.00 0.00 H
ATOM 2661 2HA NMA B 340A -46.202 27.549 -9.649 1.00 0.00 H
ATOM 2662 3HA NMA B 340A -47.159 27.918 -11.088 1.00 0.00 H
TER 2663 NMA B 340A
HETATM 2664 C1 UNK 0 -23.832 42.579 9.746 1.00 0.00 C

4

Hi Sanah,

okay, loogs good with the ligand. Then NMA is the issue here with resid 340A - changing to 341 and renaming to NME might help.

5

I am trying to generate a .str file using CGenFF. My ligand has the Se atom.
It shows the following error:
Now processing molecule UNK …
attype warning: element not supported;
skipped molecule.

6

Simply put, CGenFF does not support selenium so you cannot use this force field, unless you manually develop the necessary parameters yourself.

7

@jalemkul Thank you. It is now sorted.
while adding ions. it showed the following error.
Generated 66298 of the 100576 1-4 parameter combinations

ERROR 1 [file unk.itp, line 43]:
No default Bond types

ERROR 2 [file unk.itp, line 67]:
Duplicate atom index (27) in bonds

ERROR 3 [file unk.itp, line 67]:
No default Bond types

ERROR 4 [file unk.itp, line 131]:
No default U-B types

ERROR 5 [file unk.itp, line 133]:
No default U-B types

ERROR 6 [file unk.itp, line 170]:
Duplicate atom index (27) in angles

ERROR 7 [file unk.itp, line 170]:
No default U-B types

ERROR 8 [file unk.itp, line 174]:
No default Proper Dih. types

ERROR 9 [file unk.itp, line 176]:
No default Proper Dih. types

ERROR 10 [file unk.itp, line 182]:
Duplicate atom index (27) in dihedrals

ERROR 11 [file unk.itp, line 182]:
No default Proper Dih. types

ERROR 12 [file unk.itp, line 183]:
Duplicate atom index (27) in dihedrals

ERROR 13 [file unk.itp, line 183]:
No default Proper Dih. types

ERROR 14 [file unk.itp, line 186]:
No default Proper Dih. types

ERROR 15 [file unk.itp, line 187]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNK’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 23871]:
System has non-zero total charge: -3.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.

There were 2 notes

Program: gmx grompp, version 2020
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1927)

Fatal error:
There were 15 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

8

There is likely a .prm file (GROMACS topology format) that your ligand requires. See http://www.mdtutorials.com/gmx/complex/index.html for the protocol for updating your topology correctly.

1 Like