Dear Amber Community,
I need to parameterize modified amino acids. As a reference, I tried to learn the procedure by applying the below steps to derive the charges for Tyr, but I get charges very different from what is given in FF14SB. Am I doing something wrong? If not, how can I make comparisons between simulations using the FF14SB charges for Tyr and simulations with my modified Tyr, if the procedure for the latter can’t reproduce the charges for the former?
Step #1: Build ACE-TYR-NME capped peptide with LEaP.
Step #2: Generate alpha-helix and beta-sheet Conformers by setting phi/psi angles with CPPTRAJ
Step #3: Convert mol2 from CPPTRAJ for each conformer to Gaussian input and run with the route line: #p opt=modredundant freq hf/6-31g(d) pop=mk iop(6/33=2,6/42=6)
where I’ve defined the phi/psi angles to be fixed at the canonical alpha-helix or beta-sheet values.
Step #4: Extract ESP data from Gaussian output with espgen and concatenate results for alpha-helix and beta-sheet conformers.
Step #5: Run residuegen with the below input file, in which I’ve specified the charges of the backbone N, H, C, and O atoms to be the values found for TYR in ff14SB.
INPUT_FILE TYR.ahelix.ac
CONF_NUM 2
ESP_FILE TYR.esp
SEP_BOND N1 C2
SEP_BOND C11 N2
NET_CHARGE 0
ATOM_CHARGE N1 -0.4157
ATOM_CHARGE H4 0.2719
ATOM_CHARGE C11 0.5973
ATOM_CHARGE O3 -0.5679
PREP_FILE: TYR.prep
RESIDUE_FILE_NAME: TYR.res
RESIDUE_SYMBOL: TYR
Below is the comparison of the charges in ff14SB versus what I obtain:
TYR (ff14SB TYR (residuegen)
-0.4157 -0.4157
0.2719 0.2719
-0.0014 -0.0942
0.0876 0.1087
-0.0152 0.7629
0.0295 -0.2468
0.0295 -0.2468
-0.0011 -0.0982
-0.1906 -0.0371
0.1699 -0.0366
-0.2341 -0.0314
0.1656 0.0017
0.3226 0.1955
-0.5579 -0.2451
0.3992 0.1849
-0.2341 -0.0314
0.1656 0.0017
-0.1906 -0.0371
0.1699 -0.0366
0.5973 0.5973
-0.5679 -0.5679
Please let me know if you need more information to help me with this matter.
Best,
Matthew
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Received on Sat Dec 25 2021 - 16:30:02 PST
