GROMACS version:
GROMACS modification: Yes/No
Here post your question: How to generate ligand .gro file .itp file and .prm file for OPLS force field by using Gromacs via gromacs/share/top/oplsaa.ff/ —> vi aminoacids.rtp
How?? to perform and create my ligand OPLSAA ff i have tried from LigParGen and TopolGen also but i got different error in each ff used atomtype 900 and atomtype opls_810.
so i am asking how to do from gromacs above mention method.
these images error after using the LigParGen and their .itp file during use this CMD: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Did you visit the URL specified in the error message? The solution is there.
Thanks sir for replying.
yes sir but i don’t understand that point so can you please elaborate it, its online generated file from LigParGen.
How i will create ligand topology file from gromacs or how i will write it?? share me some tutorial based on the OPLS AA FF
If your topology introduces new atom types (or any force field parameters), the #include statement that calls it must precede any declaration of a [moleculetype]. Basically, the entire force field has to be established before any molecule can be created within it.
While my tutorial is written for CHARMM, the procedure is exactly the same: Protein-Ligand Complex
thank you Justin sir for your quick response.
After your suggestion i have added ‘prm’ into topology file but again i get same error
like
After that when i am again running my cmd then it shows this error in below image
i have used different prm file
then it shows this error:
WARNING 1 [file unk.prm, line 1]:
Too few gb parameters for type !
so i have changed this ! → ;
same error come in line third so i have change again with ;
after adding the semicolon in before BOND same error will come
then after i used the different “param” file and changes done in the topology file, also added the semicolon in whole file then after again i get this error as shown in below image
after adding semicolon in each line of unk.itp file again it shows starting error as shown below figure
sir i apologize for disturbing you, i have face this issue many times whenever i am doing simulation with OPLSAA FF
i am sharing my work file please Go through let me know where i am doing mistake;
topol.top (1.4 MB)
i am very thankful to you for helping me!!
Most of the parameter files you’re showing are not for use with GROMACS. Only the last one is, and you’ve got all the lines commented out, which renders it nonfunctional. You can’t use files for AMBER, NAMD, or CHARMM. Only use GROMACS-compatible files.
Thankyou sir for quick respond
How i proceed to next step along with this param file and what i do to remove this errror.
thanyou for your valueable response
I suggest you follow their tutorial: LigParGen Server
If there are auxiliary files they provide, they must be in GROMACS format, and as I said before, to add parameters, you must #include that topology file immediately after the parent force field.
The *q.prm files are not GROMACs .prm files but are parameters for Q-chem (hence the ‘q’ in the name). Example ligpargen/Q.py at edc5445a57f858e800baa818cd5f6b3cdaa76ea9 · Isra3l/ligpargen · GitHub. Actually Q software might not even be Q-chem? qligfep/charmm2Q.py at master · qusers/qligfep · GitHub
@jalemkul is there a program to convert Q-chem q.prm files to GROMACs prm files? There is actually a *charmm.prm file from ligpargen. This might be better input for conversion to GROMACs prm file if there exists a converter already.
Now that I re-read everything I just wrote, I don’t think ligpargen will create something like that of the jz4.prm file with “new dihedral parameters” that comes out of cgenff_charmm2gmx.py. All this information is inside the *.gmx.itp file from ligpargen.
I guess a better question is why does cgenff_charmm2gmx.py output this “*.prm” in the first place without at least adding comment that these keys, [ bondtypes ], [ angletypes ], [ dihedraltypes ] (proper and improper) are really typically inside the ffbonded.itp files of the force field(s). The bonded parameters (i.e. bonds, bond angles, improper and proper dihedrals) are listed in ffbonded.itp
Because there is no requirement to do things this way. Parameters can be added from any source, as long as the correct topology structure is observed. Parameters that appear in the .prm file from the CGenFF conversion script have not necessarily been validated or optimized in any way, so adding them to ffbonded.itp or even mentioning that maybe they should be would be extremely misleading, especially to new users who may start trying to hack those files.
Dear gromacs users, I’m working protein ligand binding simulation. I can’t prepare ligand topology, my ligand is ZnALA(Lipoic acid and Zn complex)
My problem is the ligand molecule
I can’t upload a file in ligand mol2 format to sites like Swisparam, LigPerGen, because the ligand I’m using contains an organic molecule and a metal
