[AMBER] MMPBSA with implicit radii error

From: King Wu via AMBER <amber.ambermd.org>
Date: Fri, 12 Aug 2022 12:05:50 -0700

*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,
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Received on Fri Aug 12 2022 - 12:30:04 PDT
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