GROMACS version:2022.4

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Dear all,

I want to run MD simulation on the the following molecule. The problem is the carbonyl angles here are close to 90 degrees. I tried generating the topology files for the system using ligapargen, acpype and gaff, but every time the angles are near 120 degrees. Is that a problem for my simulation and if yes, how can I overcome the issue ?

Thanks and regards

Bijaya

did you optimise the structure?

yes. Initially I did optimize. The above structure is optimized at MP2 level.

Optimization is irrelevant. The force field parameters are wrong for this case.

You can try running with the given parameters or change the equilibrium angle. My guess is that it will not make a significant difference as the structure is very rigid.

try manually rotate the angles and re-optimise the structure. if it return to the current geometry, you need to use the given paramters.

if I change the angles manually , I have to change the k values and diheadral and all the parameters associated with it, right ?

I’m afraid , can you please explain what you mean by manually rotating the angles. I need the structure with the angles 90 degrees only. So, once i generate parameters right, the .gro file I get, visualization shows the angles to be 90 only. Its the .itp file , where its around 120 degrees.Why is this mismatch ?

This is how strain energy comes about. The force field is right - sp2 carbons are at minimum energy with roughly 120 degree angles. This molecule will have a high potential energy because the angles are far from optimal.

Is the molecule’s conformation stable in molecular dynamics?

yes. It is stable. The .gro file have obtained from acpype shows angles similar to the optimized one from ab initio.

Also is there any paper/ reference I can read for a better understanding of this ?