Hi all,
I'm totally confused about the RESP charge for the ligand when performing MD calculation. It is recommended that the ligand's charge distribution should be obtained by fitting to the electrostatic potential calculated by HF/6-31g*. I have several questions below.
1. Why HF/6-31G* here, why not b3lyp/6-31G*?
2. In ff03, the RESP charges of amino acids are calculated by B3LYP/ccpVTZ//HF/6-31G** methods. With ff03 for the protein, should we use the same level to obtain the atomic RESP charges of the ligand or use HF/6-31G* instead?
3. If the structure of the ligand is from docking or co-crystal, is there any need to optimize it first before calculating the RESP charge? If the answer is YES, what is the level? HF/6-31G*, B3LYP/6-31G* or the higher the better?
4. When calculating the electrostatic potential, what is the IOp settings? I noticed that when one uses antichamber to generate the Gaussian input file, the default IOp is "iop(6/33=2, 6/42=6)". But someone told me that "iop(6/33=2,6/42=17,6/41=10)" may be better. The charges vary a lot when different iop settings are used. What is your opinion about this?
Many thanks,
Mu Xia,
Zhejiang University, China
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Received on Mon Oct 15 2012 - 07:30:04 PDT
