I am getting a fatal error in gromacs while creating a GRO file and ligand topology file under the amber force field. The acype of python providing the error message.
Parameter was:
Charge = 0
Multiplicity = 1
Force Field = 'gaff'
How can I fix atoms with the same coordinate? Kindly, provide your wise suggestions.
I am a bit confused about your question. I do not see the warning or error in the output.
Anyway, you may not install AMBER and you cannot run it. Or if you have several atoms at the position, you can use some software such as discovery studio to pre-optimize it, or manually put the atoms in the right positions.
To run acpype.py you must have amber installed in your system as it uses antechamber module of amber. So I suppose that must be the problem.
I am a bit confused about your question. I do not see the warning or error in the output.
Anyway, you may not install AMBER and you cannot run it. Or if you have several atoms at the position, you can use some software such as discovery studio to pre-optimize it, or manually put the atoms in the right positions.
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