*Hello AMBER and MMPBSA experts, *
*I used CHARMM-GUI to build a membrane bound protein with ligand to have
100ns MD traj. Now I am calculating using MMPBSA in AMBER.*
*1. I used cpptraj to strip waters, ions, and POPC membrane, the resulting
files are complex.prmtop and complex.dcd.*
*2. I used ante-MMPBSA to generate rec.prmtop and lig.prmtop and --radii
mbind3, I did not get com.prmtop, i think because the com.prmtop is the
same as complex.prmtop.....*
*3. Then error comes in when i run: *
$MMPBSA.py -O -i mmpbsa.in -o mmpbsa_first50ns.out -cp com.prmtop -rp
rec.prmtop -lp ligand.prmtop -y complex_first50ns.dcd > run_first50ns.log
-eo mmpbsa_first50ns.csv
$ File "/home/apps/amber20_src/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/home/apps/amber20_src/lib/python3.9/site-packages/MMPBSA_mods/main.py",
line 611, in loadcheck_prmtops
self.normal_system.CheckConsistency()
File
"/home/apps/amber20_src/lib/python3.9/site-packages/MMPBSA_mods/parm_setup.py",
line 907, in CheckConsistency
raise PrmtopError('Topology files have no Implicit radii! You can ' +
PrmtopError: Topology files have no Implicit radii! You can add implicit
radii using xparmed.py or parmed.py
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.
*4. BTW, in the mmpbsa.in <
http://mmpbsa.in> input file, I specified both
radiopt=0 and 1 to try, and still got the error. Can someone tell me how to
fix it?*
&general
startframe=1,
endframe=5000,
interval=50,
verbose=2,
keep_files=1,
/
&gb
igb=5,
saltcon=0.15,
surften=0.0072,
surfoff=0.0000,
/
&pb
radiopt=0,
istrng=0.15,
fillratio=4.0,
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 12 2022 - 12:30:04 PDT
