GROMACS modification: Yes/No
Here post your question I got extra number in the topol.top file than solv.gro and this have when I just add solv step. how can i solved it.
number of coordinates in coordinate file (protein_ligand_solv.gro, 61506)
does not match topology (topol.top, 80980)
The error means you haven’t properly kept track of the contents of the system. Almost all bookkeeping can be done automatically (water and ions), but if you have a ligand as you appear to, you have to make careful manual adjustments to the coordinate and topology files. If one changes, so too must the other.
It is not possible to diagnose the origin of this problem without a complete listing of the commands issued to this point and a detailed description of any other manual modifications you have made. Otherwise, it is simply “you haven’t kept track of things properly.”
The steps as following
Parmchk2 –i ligand_gaff.mol2 –f mol2 –o ligand.frcmod
saveamberparm MOL ligand.prmtop ligand.inpcrd
Savepdb MOL ligand_amber.pdb
tleap -f commands.in
acpype -p ligand.prmtop -x ligand.inpcrd -b ligand
gmx pdb2gmx -f protein.pdb -o protein.gro -ignh -ter -p protein.top
I used OPLS-AA/L
I used NH3 and COO-
water model: I used #1 that is recommended
cat protein.gro ligand_GMX.gro > protein_ligand.gro
Vi protein_ligand.gro and add the number manually of the protein and ligand
cp ligand_GMX.top ligand.itp
take the atomtypes from ligand.itp and add it to topol.top under forcfield
take the last line of ligand.itp and delete the section of system and ligand
add it to topol.top
gmx editconf -f protein_ligand.gro -o protein_ligand_box.gro -bt cubic -d 1.0 -c
gmx solvate -cp protein_ligand_box.gro -cs spc216.gro -p topol.top -o protein_ligand_solv.gro
download the ions.mdp
gmx grompp -f ions.mdp -c protein_ligand_solv.gro -p topol.top -o protein_ligand_ions.tpr
after that the error message appears
I cannot identify the source of such a massive disparity; something else must have happened (i.e. you repeated a step somewhere or mismanaged files). I would suggest simply starting over, and at every step, after each command you enter or modification you make, you verify that the topology and coordinates are in sync.
Also note that it is inappropriate to generate an AMBER topology for a ligand and try to mix it with the OPLS-AA force field for the protein. You need to use a self-consistent force field for everything, otherwise the results (if you can even get past the syntactical issues) will be nonsensical.
What is the the commands to generate topology for a ligand using OPLS-AA force field.
In case of AMBER forcefield, I used Parmchk2 –i ligand_gaff.mol2 –f mol2 –o ligand.frcmod
Still I cann’t solve the proble. I use amber force field and everything goes well until i reach to the add ions
The command is gmx grompp -f ions.mdp -c protein_ligand_solv.gro -p topol.top -o ions.tpr
and the error message is WARNING 17 [file topol.top, line 42]:
Atomtype H4 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
I also attach the topol.top and itp files
topol.top (833.6 KB)
This is your problem:
[ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb N3 N3 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CX CX 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 HP HP 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 HC HC 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 NA NA 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CW CW 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CN CN 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 C* C* 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
You are redefining atom types that already exist in the force field. The simple solution is - don’t. If the ligand already uses known atom types, you don’t need to add them in again.
Thank you. Also, is there any way to make the MD simulation faster since it took 3 days and my computer is on and the work didn’t complete yet
MD simulations are computationally expensive. Common laptop or desktop hardware are not suited for running them. You need high-performance computing clusters or specially designed GPU workstations to reasonably run most MD. GROMACS can run on a laptop, but generally speaking, it shouldn’t.
I transferred all of my files to super computer and I am traying to run the production using this command: gmx_mpi mdrun -deffnm receptor_ligand_prod &
Howeverver there is an error message: -bash: gmx_mpi: command not found
How can I solved? Please let me know.
You need to speak to your system administrator to understand how to configure your environment. Simply put, the
gmx_mpi binary is not in your environment’s
$PATH. How you rectify that depends on the cluster itself, and that’s something an admin can tell you.
Ok. Will ask them. Thanks a lot