[AMBER] Questions about QM/MM simulations

From: 马芳芳 <mafangfang0411.mail.dlut.edu.cn>
Date: Thu, 6 May 2021 09:55:39 +0800 (GMT+08:00)


Recently, I am trying to simulate CF3CF2CO2- anions reaction with superoxide radicals (O2-) in aqueous solution by using QM/MM calculations. The net charges are -2.

Gas phase was firstly employed to simulate the above reactions. When creating the pdb files, I used two different methods to define the charges of the CF3CF2CO2- and O2-. I used antechamber command with -nc to define the charges. However, no charge was defined in the .mol2 files. Therefore, the NBO charges calculated by Gaussian were selected to define the charges. Using the above two methods(antechamber with -nc and NBO charges)to create the pdb files, we got two different QM/MM results. According to my understanding, since the QM part can calculate the charges, charges should not have impacts on the QM/MM results. Would you please so kind to give me some suggestions?

Secondly, aqueous solution without adding counterions was used and the NBO charges were used to create the pdb files. I found that it can get the similar results with the gas phase with NBO charges. However, when the counterions were added, the results are different. Now, I don’t know which result is reliable. Maybe the result of aqueous solution with counterions and NBO charges is more reliable. Would you please so kind to give me some suggestions about my input files (aqueous solution with counterions and NBO charges)? Does periodic boundary conditions (TIP3PBOX used) affect the results?

Attached are the input files.

Thank you very much! I am looking forward to your reply.

Best wishes!

Fangfang Ma

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Received on Wed May 05 2021 - 19:00:02 PDT
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