GROMACS version: 2021.4
GROMACS modification: Yes/No
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Could anyone help me with creating the topology files for the ligand GROMOS96 43a1 force field.
When I try to create the topology file for the ligand using the command “gmx pdb2gmx -f new_ligand.pdb -o ligand_processed.gro -p ligand.top” it says that “Residue ‘UNK’ not found in residue topology database”.
You need to derive the parameter for your molecule and include it in the parent topology.
You may generate topology from here. Following the protein-ligand tutorial is your guide.
I tried using the ATP webserver for the topology generation of the ligand but it gives me the following error.
Your job that was submitted at 04:29:37 on 2024-03-14 (ID 1625342) terminated with the following error: Unsupported bond length encountered: 0.34nm (C23-H19). This often indicates there is an error in the submitted structure.
Depending on the specific nature of the error, template results may be available (http://atb.uq.edu.au/molecule.py?molid=1625342). This molecule will be deleted in 7 days.
This is my ligand pdb file.
HETATM 3728 C UNK N 1 3.272 2.876 17.206 0.00 0.00 C
HETATM 3729 C UNK N 1 2.255 2.662 16.250 0.00 0.00 C
HETATM 3730 C UNK N 1 2.332 3.352 15.022 0.00 0.00 C
HETATM 3731 C UNK N 1 3.422 4.240 14.781 0.00 0.00 C
HETATM 3732 C UNK N 1 4.378 4.388 15.821 0.00 0.00 C
HETATM 3733 C UNK N 1 3.618 4.994 13.571 0.00 0.00 C
HETATM 3734 C UNK N 1 5.467 5.248 15.679 0.00 0.00 C
HETATM 3735 C UNK N 1 4.727 5.848 13.466 0.00 0.00 C
HETATM 3736 C UNK N 1 5.645 5.978 14.511 0.00 0.00 C
HETATM 3737 C UNK N 1 3.251 2.215 18.521 0.00 0.00 C
HETATM 3738 C UNK N 1 4.361 2.299 19.379 0.00 0.00 C
HETATM 3739 C UNK N 1 4.323 1.673 20.633 0.00 0.00 C
HETATM 3740 C UNK N 1 6.638 3.139 19.737 0.00 0.00 C
HETATM 3741 C UNK N 1 6.587 2.440 21.091 0.00 0.00 C
HETATM 3742 C UNK N 1 7.798 2.556 18.921 0.00 0.00 C
HETATM 3743 C UNK N 1 6.870 4.634 19.976 0.00 0.00 C
HETATM 3744 C UNK N 1 5.506 1.767 21.500 0.00 0.00 C
HETATM 3745 C UNK N 1 3.170 0.973 21.036 0.00 0.00 C
HETATM 3746 C UNK N 1 2.064 0.902 20.176 0.00 0.00 C
HETATM 3747 C UNK N 1 2.107 1.518 18.923 0.00 0.00 C
HETATM 3748 C UNK N 1 1.103 1.710 16.552 0.00 0.00 C
HETATM 3749 C UNK N 1 -0.180 2.461 16.814 0.00 0.00 C
HETATM 3750 C UNK N 1 -1.291 2.333 16.045 0.00 0.00 C
HETATM 3751 C UNK N 1 -2.545 3.079 16.419 0.00 0.00 C
HETATM 3752 C UNK N 1 -1.365 1.427 14.835 0.00 0.00 C
HETATM 3753 O UNK N 1 4.263 3.715 16.956 0.00 0.00 O
HETATM 3754 O UNK N 1 1.466 3.170 14.190 0.00 0.00 O
HETATM 3755 O UNK N 1 5.468 2.988 18.993 0.00 0.00 O
HETATM 3756 O UNK N 1 3.128 0.374 22.245 0.00 0.00 O
HETATM 3757 O UNK N 1 2.792 4.938 12.501 0.00 0.00 O
HETATM 3758 O UNK N 1 6.706 6.804 14.402 0.00 0.00 O
HETATM 3759 H UNK N 1 3.332 -0.565 22.356 0.00 0.00 H
HETATM 3760 H UNK N 1 2.982 4.534 11.651 0.00 0.00 H
HETATM 3761 H UNK N 1 6.662 7.630 13.898 0.00 0.00 H
Could you help me resolve the issue.
Thank you
Optimise the structure using QM before submitting to ATB
Are there any online free tool that I can use for optimizing the structure using QM?
You can use avogadro to optimise at MM level. It is better to do geometry optimisation using QM softwares like gaussian or QChem etc. Im not aware of any online tool.
I used Avogadro and it did work.
Thank you
But now while I’m getting the files generated by ATB webserver it gives me files for GROMOS54a7 but I want to use GROMOS96 43a1 as that is what I have used for my protein of interest. Is it okay if I use the GROMOS54a7 files for ligand and GROMOS96 43a1 for protein??
It is not adviced to use different force field, here both can give different dynamics of the proteins.
my question is why GROMOS FF?
I have just taken the reference from already published article, where they have used GROMOS96 43a1 as the force field. As I am new to MDS, I am not sure on how to go about it.
So is there any way I can get GROMOS96 43a1 force field topology files for the ligand or should I use GROMOS54a7 itself for the protein as well??
If ATB server not providing you 43a1 which is older than 54a7, i dont know other way to get paramters or any other servers. In any case if you want to stick with gromos use 54a7, force field selection for your protein should be based on the existing literature or based on your understanding about the problem you are addressing. Try to use CHARMM-GUI .
Thank you for your suggestion sir.