In this tutorial we are going to leran hoe to parametierize PEG2000-DMG using RESP method.
PEG2000-DMG is a large, artificial lipid consisting of 414 atoms. This molecule is used as a lipid additive for the Moderna Covid Vaccine's lipid nano particle (LNP).
First, we need to generate the 3D structure of PEG2000-DMG. In this tutorial, we use the structure from PubChem (PubChem ID 10257450). Because the structure was generated from a 2D sdf file, we need to optimize it manually for faster results, then optimized with semiempirical AM1 approximation.
Next, we need to divide the optimized structure into several fragment molecules. In this tutorial, we will divide the structure into four fragments: 13C, 14L, EG, and TC.
Next, each of the fragments were further optimized using DFT/B3LYP/6-311++G and then continued with a single point energy calculation using HF with IOp(6/33=2,6/41=10,6/42=17,6/50=1). (For better results, I recommend using DFT or MP2 or MP4 instead of HF.)
Next, generate the esp file
espgen -i x_HF.log -o x.esp
After that, the ac file
antechamber -fi gout -fo ac -i x_HF.log -o x.ac
and generate the RSEP file inpput using the ac file
respgen -i x.ac -o x_resp.in -f resp1 -e 2
respgen -i x.ac -o x_resp2.in -f resp2 -e 2
Then, calculate the RESP to obtain the final atomic charge
resp -i x_resp.in -o x_resp.out -p x_resp.pch -t EGT_resp.ach -e x.esp -s esot1
resp -i x_resp2.in -o x_resp2.out -p x_resp2.pch -t x_resp2.ach -e x.esp -s esot2 -q x_resp.ach
Now, we have all the atomic charges and ac files of the fragments.
antechamber -i x.ac -fi ac -o x_resp.ac -fo ac -c rc -cf x_resp2.ach
Finally, we need to combine all the fragments, charges, and atom types to obtain the parameterized PEG2000-DMG molecule.
Happy!