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Atomic number set to 0 #20
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That number is not relevant as the correct values are set in the [atoms] section. |
@selimsami Thanks for the explanation, I use |
Oh, that is not great. This is the line that needs to be changed to fix this issue. |
@selimsami It seems that the problem is here qforce/qforce/molecule/non_bonded.py Line 579 in 6fb8fe1
So if line[-6].isdigit() is not a digit, the atomic number is set to zero. So the definition of atomic number in Gromacs atomtype is optional, so gaff and gaff2 currently don't have the atomic number defined. This is because the atomic number is not defined in the amber topology. I think there could be two ways of solving this problem.
I wonder what do you think? |
I like option 1 more. but please see my comment to #21 |
This issue is fixed with merging of #21 |
In my test case, I got the atomic number in atomtypes to zero.
The setting file is like
I wonder if this is a TODO or is a bug? I could try to make an example if this is not something that I would expect.
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