You have mismatching residue names in the .mol2 and .str files. In the .mol2 it's called (whatever that means) and since CGenFF subsequently couldn't find a valid string, the default name "Molecu" is applied in the residue definition. You need matching residue names in both files.  Note you have significant penalties for charges and all bonded interactions, which means this topology requires significant work before it can be considered reasonable to use in an MD simulation.

Thank you for your kind consideration.

my problem solved and about charges I know about that , i try simulate of docking process and i need this interaction and charges(i think so).

but i'm not sure about that. do you have any suggest for this matter??? 

Yours sincerely

Most docking programs have their own methods for calculating partial charges. I don't do docking so I can't advise you on that.

what??

Dear Justin Lemkul

"cgenff_charmm2gmx-1.py" couldn't complete itp file,dihedral section is terminated.

Do you know why??? i couldn't solve it

Best Regard

Was there any error message?

No ,all file generated and no error found in terminal .

Well, jz4.itp appears to contain a different molecule than your original files that you posted to this issue (ajz4.*). So if there's no error, then the dihedrals are right. Everything looks fine to me.

Yes I tried simulation by different system and all of that have same error.

i try with other system and take a previous error.

some one said about that this error comes from "force field you're trying to use does not have a dihedral term for that type of dihedral"

last line that error appear is " gmx grompp -f em.mdp -c solvated.pdb -p topol.top -o ions.tpr"

best regard

Note that jz4.str includes two new dihedrals; these must be the missing parameters that grompp complains about. The conversion script will write a .prm file that has these parameters, and it must be #included like anything else, before the declaration of any [moleculetype]. As for the fatal error, it is quite clear that you simply didn't update the topology after adding water.  Let gmx solvate do that for you by using the -p flag. See simple tutorials for examples.

i used this tutorial "http://rossi.chemistry.uconn.edu/workshop/charmm-gromacs-small-organic-molecules.html" but my problem didn't solve.

i don't know other tutorial, if you know or have a correct tutorial please let me know.

you are professional in this field,please write a correct tutorial and solve this problem for ever.

best regard

I would suggest my own tutorial, but it appears that the author of the linked tutorial has effectively copied my tutorial and changed a few things about it. It does instruct you to use -p when running gmx solvate, which clearly you did not do. The part that you're missing with respect to the parameters is that the tutorial does not completely describe the correct topology modifications.

"Modify the topo.top file generated for the protein to include the required files for the ligand." But the author does not state what this entails. You need to:

1. Add a line: #include "jz4.prm" immediately after the first #include statement for the force field

2. Add a line: #include "jz4.itp" (which can be located just about anywhere).

i used this command " gmx solvate -cs -cp boxed.pdb -o solvated.pdb -p topol.top"

Dear Justin Lemkul

my problem solved :-)

Thank you very much; your support is greatly appreciated.

Best Regard