GROMACS version: 2022.4
GROMACS modification: Yes/No
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Hello,
I calculated some partial charges with Maestro, Schrodinger for n-octanol and i would like to convert a .mae or a .mol2 file in a .gro file that includes the partial charges for this molecule but i had some errors appeared. In particular i take this message in terminal
Error in user input:
Invalid command-line options
In command-line option -f
File ‘/mnt/data_2TB/maestro_OCTANOL_partial_charges/octanol.mol2’ cannot
be used by GROMACS because it does not have a recognizable extension.
The following extensions are possible for this option:
.gro, .g96, .pdb, .brk, .ent, .esp, .tpr
In command-line option -ff
Too many values
PRODRG is not currently working, i have also tried with obabel and antechamber but i cannot make a .gro file.
Is there anything else i could try?
Thank you for your time!
For coordinates, you do not need a .gro file. A .pdb file will work fine. I suspect any program that can write a .mol2 can write a .pdb. I suspect you will have some issue with parameters later, but this question seems focused on coordinates and using a .pdb should solve your issue. If you really cannot write a .pdb from your other software, then you can load your .mol2 into VMD and save the coordinates as a .pdb.
Thank you, coordinates are then fixed.
But i would also like to include these specific values of partial charges at a .gro file, that’s why i am wondering.
Have you got any idea about that?
Perhaps start with some tutorials on Gromacs (running and making parameters)? You sound like possibly a new Gromacs user and parameterization is not the simplest thing one can do in MD. Hint: the charges do not go in the structure file.
That’s right i am a new user and I may making the question more difficult.
I am talking about how to make a topology file for octanol like this tutorial Building Biphasic Systems
Charges of atoms seem to appear at the topology file given.