How and why werethe charges changed in the topology file of the ligand? Also after simulation I found my ligand and protein were far apart from each other (observed in simulation movie; i.e. they were not interacting with each other). Kindly suggest the plausible reason for this and how can I rectify it.
About the charge query,
Let's take a look at the [ atoms ] section of our JZ4 topology:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 JZ4 C4 1 0.000 15.0350
2 CH2 1 JZ4 C14 2 0.059 14.0270
3 CH2 1 JZ4 C13 2 0.060 14.0270
4 C 1 JZ4 C12 2 -0.041 12.0110
5 CR1 1 JZ4 C11 2 -0.026 12.0110
6 HC 1 JZ4 H11 2 0.006 1.0080
7 CR1 1 JZ4 C7 2 -0.026 12.0110
8 HC 1 JZ4 H7 2 0.006 1.0080
9 CR1 1 JZ4 C8 2 -0.026 12.0110
10 HC 1 JZ4 H8 2 0.007 1.0080
11 CR1 1 JZ4 C9 2 -0.026 12.0110
12 HC 1 JZ4 H9 2 0.007 1.0080
13 C 1 JZ4 C10 3 0.137 12.0110
14 OA 1 JZ4 OAB 3 -0.172 15.9994
15 H 1 JZ4 HAB 3 0.035 1.0080
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 JZ4 C4 1 0.000 15.0350
2 CH2 1 JZ4 C14 2 0.000 14.0270
3 CH2 1 JZ4 C13 2 0.000 14.0270
4 C 1 JZ4 C12 2 0.000 12.0110
5 CR1 1 JZ4 C11 3 -0.100 12.0110
6 HC 1 JZ4 H11 3 0.100 1.0080
7 CR1 1 JZ4 C7 4 -0.100 12.0110
8 HC 1 JZ4 H7 4 0.100 1.0080
9 CR1 1 JZ4 C8 5 -0.100 12.0110
10 HC 1 JZ4 H8 5 0.100 1.0080
11 CR1 1 JZ4 C9 6 -0.100 12.0110
12 HC 1 JZ4 H9 6 0.100 1.0080
13 C 1 JZ4 C10 7 0.150 12.0110
14 OA 1 JZ4 OAB 7 -0.548 15.9994
15 H 1 JZ4 HAB 7 0.398 1.0080
ATB and PRODRG servers are the best tools for creating ligand topology files.you don't need to modify their partial charges.Just dock protein and ligand before simulation.separation after docking (during simulation) represents wrong initial docking pose!
If you sure about accuracy of topology file generation procedure restart your simulation with different docking pose.
Best
How do you simulate? BD/SD with implicit sovent or MD with explicit solvent? How does the initial configuration look like?
Best regards
You did molecular docking? If the answer is positive you need to check the condition of the docking ligand or it may not have an affinity for the target.
If the ligand was crystallized in the molecule (pdb file) their dynamics needs to be redone. I have news that ligands out of protein, except in very special conditions as strong steric effect.
Parameters such charges do not change in the topology file. However, if you recalculate them after a dynamic, obviously these values are not the same. I do not believe that the reason of the problem is this.
regards
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