When I'm building a system and trying to run minimization, it shows some warnings like this:
"Warning: atom name 1 in topol.top and test_box.gro does not match (C1 - C5)".
I found that the order of atoms in *.gro is different from *.top, do I need to change that so that they are matched to each other? Thanks.
Well, I'm having the same trouble myself.
In a prior aplication I solved this by changing the atom order in the .gro file, but that was when the involved molecule was the ligand. Now I'm having this trouble with one of the solvents (as I'm using an ethanol/water mix) and changing every single of the 800 EtOH molecules is just not in my plans any soon.
So, if anyone knows a better way of having both files matching atom order, I'd be infinitely grateful.
Well, I'm having the same trouble myself.
In a prior application I solved this by changing the atom order in the .gro file, but that was when the involved molecule was the ligand. Now I'm having this trouble with one of the solvents (as I'm using an ethanol/water mix) and changing every single of the 800 EtOH molecules is just not in my plans any soon.
So, if anyone knows a better way of having both files matching atom order, I'd be infinitely grateful.
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