Dear AMBER Users,
Hello, I am trying to run a alanine scanning of the protein EGFR, which is connected to the ligand Lapatinib.
After making the required .prmtop files, I went through the following command:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp EGFR_FMM_solvated.prmtop -cp EGFR_FMM.prmtop -rp EGFR.prmtop -lp FMM.prmtop -y *.mdcrd -mc EGFR_FMM_mutant.prmtop -mr EGFR_mutant.prmtop
and I got the following error:
Loading and checking parameter files for compatibility...
File "/home/hjs/MD/amber24/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File "/home/hjs/MD/amber24/lib/python3.11/site-packages/MMPBSA_mods/main.py", line 652, in loadcheck_prmtops
self.normal_system.CheckConsistency()
File "/home/hjs/MD/amber24/lib/python3.11/site-packages/MMPBSA_mods/parm_setup.py", line 931, in CheckConsistency
raise PrmtopError('Inconsistent charge definition for atom %d!' %
PrmtopError: Inconsistent charge definition for atom 4747!
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
After this, I checked with parmed:
The original EGFR+FMM(protein-ligand complex) file's mask .4747 looked like this:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass Charge GB Radius GB Screen
4747 290 MOL P1 p5 15 2.1000 0.2000 30.9700 1.2430 1.8500 0.8600
While the mutant one (LYS196 changed to ALA) looked like this:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass Charge GB Radius GB Screen
4747 292 MOL O1 o 8 1.6612 0.2100 16.0000 -0.6513 1.5000 0.8500
So, how does this "mask" system work, and why does the mask .4747 points to different atoms?
The original EGFR+FMM file looks like:
ATOM 3074 HG SER A 195 28.092 42.091 22.178 1.00 31.68 H
ATOM 3075 N LYS A 196 30.381 40.198 25.948 1.00 35.98 N
ATOM 3076 CA LYS A 196 30.998 40.103 27.264 1.00 36.17 C
ATOM 3077 C LYS A 196 31.857 41.352 27.423 1.00 36.37 C
ATOM 3078 O LYS A 196 32.656 41.681 26.543 1.00 36.66 O
ATOM 3079 CB LYS A 196 31.878 38.854 27.355 1.00 37.51 C
ATOM 3080 CG LYS A 196 31.041 37.603 27.084 1.00 37.84 C
ATOM 3081 CD LYS A 196 31.930 36.367 27.201 1.00 40.09 C
ATOM 3082 CE LYS A 196 32.370 36.197 28.656 1.00 41.89 C
ATOM 3083 NZ LYS A 196 33.435 35.160 28.749 1.00 43.62 N
ATOM 3084 H LYS A 196 30.914 39.756 25.199 1.00 35.98 H
ATOM 3085 HA LYS A 196 30.242 40.030 28.046 1.00 36.17 H
ATOM 3086 HB2 LYS A 196 32.693 38.920 26.634 1.00 37.51 H
ATOM 3087 HB3 LYS A 196 32.332 38.790 28.344 1.00 37.51 H
ATOM 3088 HG2 LYS A 196 30.217 37.541 27.795 1.00 37.84 H
ATOM 3089 HG3 LYS A 196 30.600 37.655 26.089 1.00 37.84 H
ATOM 3090 HD2 LYS A 196 31.388 35.482 26.867 1.00 40.09 H
ATOM 3091 HD3 LYS A 196 32.802 36.469 26.555 1.00 40.09 H
ATOM 3092 HE2 LYS A 196 32.740 37.145 29.046 1.00 41.89 H
ATOM 3093 HE3 LYS A 196 31.517 35.910 29.271 1.00 41.89 H
ATOM 3094 HZ1 LYS A 196 34.044 35.360 29.568 1.00 43.62 H
ATOM 3095 HZ2 LYS A 196 32.998 34.223 28.863 1.00 43.62 H
ATOM 3096 HZ3 LYS A 196 34.008 35.172 27.881 1.00 43.62 H
ATOM 3097 N PRO A 197 31.695 42.077 28.540 1.00 36.61 N
while the mutant file looks like:
ATOM 3074 HG SER A 195 28.092 42.091 22.178 1.00 31.68 H
ATOM 3075 N ALA A 196 30.381 40.198 25.948 1.00 35.98 N
ATOM 3076 CA ALA A 196 30.998 40.103 27.264 1.00 36.17 C
ATOM 3077 C ALA A 196 31.857 41.352 27.423 1.00 36.37 C
ATOM 3078 O ALA A 196 32.656 41.681 26.543 1.00 36.66 O
ATOM 3079 CB ALA A 196 31.878 38.854 27.355 1.00 37.51 C
ATOM 3084 H ALA A 196 30.914 39.756 25.199 1.00 35.98 H
ATOM 3085 HA ALA A 196 30.242 40.030 28.046 1.00 36.17 H
ATOM 3097 N PRO A 197 31.695 42.077 28.540 1.00 36.61 N
Thank you for your time and help.
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Received on Tue Jul 09 2024 - 17:30:02 PDT
