I have docked the protein-ligand complex. In the process of molecular dynamics by gromacs I used GROMOS96 53a6 force field for my protein. In the next step for my ligand according to GROMACS tutorial I used (Step Two: Prepare the Ligand Topology http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html ).
I need obtain two files X.itp & Y.gro. I used the ATB server. The server gave me many files (Topology Files and Structure Files). I assume that I should choose GROMOS96 files, but which one?
How can I find the coordinate file (gro file)?
http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=18789&outputType=top&atbVersion=v2Top&ffVersion=Gromos#files
If you're using Gromacs, you need the united-atom topology and coordinates. I would suggest using the "original geometry" file for coordinates, because otherwise ATB will have optimized the structure, which changes the coordinates and almost certainly will lead to clashes with the protein when you re-introduce the coordinates. To convert from .pdb to .gro, simply use editconf.
If you're using Gromacs, you need the united-atom topology and coordinates. I would suggest using the "original geometry" file for coordinates, because otherwise ATB will have optimized the structure, which changes the coordinates and almost certainly will lead to clashes with the protein when you re-introduce the coordinates. To convert from .pdb to .gro, simply use editconf.
Dear Justin,
Which software than can be used with ATP all atom topology for MD?
I don't know the purpose of all-atom files from ATB. The Gromos force fields are united-atom. Perhaps it is explained somewhere in the FAQ.
Here are some tips:
1) you don't need .gro file to start your simulation. you can easily use the original or optimized pdb file of your syste,. after finishing your first simulation (either em or md), gromacs will provide you with the .gro file.
2) For itp file, assuming you are using gromacs package, you should download files under GROMACS not the GROMOS. Don't wory about the all atom or united atom .itp as all required parameters for the bonded potentials is same in the GROMOS force field. You may only run into some problems with missing dihedral angles if you choose all atom force field.
I would tend to disagree with Abolfazi.
To point (1), while true that .gro files are not required (Gromacs happily accepts many formats), it can be very important which geometry you choose. If a docked ligand is then optimized in the absence of the receptor protein, the geometry can change substantially, leading to atomic clashes when one re-introduces the coordinates. This is very important in the case of crystallographic ligands, which generally do not have hydrogens added, so external software like ATB is necessary for building these on.
To point (2), it is very important to use only the united-atom topology! In looking at the all-atom files, it appears they are available to demonstrate how charges were summed to yield the united-atom topologies. The fact that methyl groups, for instance, use HC types for aliphatic H atoms is very concerning; HC is for aromatic H atoms only. Misapplying them can be very detrimental to the simulation. If there are missing parameters, that should set off alarm bells that something is wrong.
Thank you. I chose United-Atom PDB (original geometry) .
because I used GROMOS96 53a6 force field for my protein, I should choose coordinate and topology file from GROMOS96 Files. Is this the correct approach?
which coordinate file i should choose?, GROMOS96 United-Atom Topology or GROMOS96 United-Atom MTB ?
Dear Travis Pollard,
Is it right way if I choose GROMACS G53A6FF United-Atom (ITP file) for 53a6 force field in place of Gromos96 UA topology?
Thanks a lot !
Dear Justin Lemkul ,
I had passed a ligand containing 26 atoms through ATB server.
I have noticed that the ATB server retains only few hydrogens for United-atom topology creation. It is evident from the united atom (original geometry) pdb. (please see the attached lig_unitedatom.png). This is reflected even in the itp file as in this case only the details of 20 atoms are present.
However, in the case of all-atom files, all the atoms are considered. It retained all the atoms both in the all-atom original geometry pdb and .itp files. (attached as lig_allatom.png).
In my humble opinion, using United-atom files might give artificial interactions which are not relevant as few of the atoms are missing.
Request you to give your opinion on this.
Thank you,
Regards.
GROMOS is a united-atom force field. This is its convention. If you believe an all-atom force field is more suitable, you'll need to use the appropriate tools for it.
Gauri Thapa there is no .prm file from ATB. This is unique to the CGenFF conversion script in my tutorial (and the .prm file is really just an .itp file, which is what every server produces for GROMACS-compatible input).
Justin Lemkul Thanks a lot. I would be very happy if you could solve the error that I am getting for using gromos force-field for my ligand( generated by ATB) which, as the error says, was parameterized using multiple time stepping scheme with gromacs (which utilizes single range cut-off)
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Check if molecules in your system
are affected by such issues before proceeding.
How should I solve this ?
Thank you very much.
Gauri Thapa you don't. There are issues with how the GROMOS force fields were parametrized, which are described in full here: https://chemrxiv.org/articles/On_The_Importance_of_Accurate_Algorithms_for_Reliable_Molecular_Dynamics_Simulations/11474583/1
Thank you very much Justin Lemkul . I will go through the paper once in order to understand how to make it work.
Hi
i want to convert .pdb file build by atb server to .gro (by editconf) in gromacs but below error occured :
Number of atom in pdb file is zero.
Whats the problem?
Dear Gauri Thapa , I have untared the ATB force field to my gromacs directory but when I use the gmx pdb2gmx command the only thing that has been changed in my force fileds after running the command is appearing another GROMOS96 54a7 force field, but when I see in the directory there is a file with this name on it "gromos54a7_atb.ff", I wanted to know if I have corretlly extracted the gromos54a7_atb.ff.tar.gz or not and how do I know which one is the new force field?
thank you for your help
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