From: Xu, Shenyuan (xus2_at_miamioh.edu)
Date: Sun Sep 20 2020 - 10:55:46 CDT
Hello everyone,
I tried to mutate cysteine to farnesylated cysteine, and successfully
generated the mutation by psfgen. After I combine the protein, mg, water,
gdp using psfgen, then minimize it in namd, it showed the error "unable to
find the angle parameter". The toppar used for the farnesylated cysteine is
from "toppar_all36_lipid_prot.str".
Here is the mutation part for psfgen:
#load the topology files#
topology top_all36_prot.rtf
topology top_all36_na.rtf
topology top_all36_carb.rtf
topology top_all36_cgenff.rtf
topology toppar_water_ions.str
topology toppar_all36_lipid_prot.str
topology toppar_all36_na_nad_ppi.str
segment PRO {
first NTER
last CTER
pdb $pdbname
mutate [string trimleft $mutpos 0] CYSF
}
coordpdb $pdbname PRO
guesscoord
Here is the remarks from the psf file:
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology ../top_all36_prot.rtf
REMARKS topology ../top_all36_na.rtf
REMARKS topology ../top_all36_carb.rtf
REMARKS topology ../top_all36_cgenff.rtf
REMARKS topology ../toppar_all36_lipid_prot.str
REMARKS topology ../toppar_all36_na_nad_ppi.str
REMARKS topology ../toppar_water_ions.str
REMARKS segment PRO { first NTER; last CTER; auto angles dihedrals }
REMARKS segment GDP { first NONE; last NONE; auto angles dihedrals }
REMARKS segment MG { first NONE; last NONE; auto angles dihedrals }
REMARKS segment SOLV { first NONE; last NONE; auto none }
REMARKS defaultpatch NTER PRO:1
REMARKS defaultpatch CTER PRO:188
Here is the log file from the energy minimization that contains the error:
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../par_all36_prot.prm
Info: PARAMETERS ../par_all36_na.prm
Info: PARAMETERS ../par_all36_lipid.prm
Info: PARAMETERS ../par_all36_carb.prm
Info: PARAMETERS ../par_all36_cgenff.prm
Info: PARAMETERS ../par_water_ions.prm
Info: PARAMETERS ../toppar_all36_lipid_prot.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Warning: DUPLICATE ANGLE ENTRY FOR CD-CT2-NH2
PREVIOUS VALUES k=50 theta0=107 k_ub=0 r_ub=0
USING VALUES k=52 theta0=108 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 970 BONDS
Info: 2865 ANGLES
Info: 7022 DIHEDRAL
Info: 200 IMPROPER
Info: 6 CROSSTERM
Info: 359 VDW
Info: 77 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 95 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG331 CG2D1 CG331 (ATOMS
3000 2999 3004).
And I think the angle parameter is missing in
the toppar_all36_lipid_prot.str.
Thanks for any suggestions and comments.
Shen
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