Hello Dr Luo
Thank you for your reply. To be honest, I did not know how to use "parmed"
to add the implicit radii at this moment even after searching around the
website. However I solved the problem by using Tleap to add the implicit
radii to the *.prmtop files.
Also thanks for great references, they are worth reading.
But what if I stripped the POPC membrane, water and ions, the current
complex has only the membrane protein and ligand. Does that affect the
MMPBSA calculation? or MMPBSA will still consider it as a global protein?
On Fri, Aug 12, 2022 at 12:32 PM Ray Luo <rluo.uci.edu> wrote:
> Did you try the suggested revision: "PrmtopError: Topology files have
> no Implicit radii! You can add implicit
> radii using xparmed.py or parmed.py"? Any issue with the suggestions?
>
> In addition, you'd better follow the protocol in the following papers
> for membrane protein applications, otherwise, your MMPBSA would
> process your system assuming it's a globular protein.
>
> J. Chem. Inf. Model. 2019, 59, 6, 3041–3056
> J. Chem. Theory Comput. 2017, 13, 7, 3398–3412
>
> There is a sample input file in
> $AMBERHOME/AmberTools/test/mmpbsa_py/12_Membrane_Channel
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Fri, Aug 12, 2022 at 12:06 PM King Wu via AMBER <amber.ambermd.org>
> wrote:
> >
> > *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 <
> https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!O5HPWrqlPGC-qwrlP4IfT3prL6nCy0OZ_uo0iA8PjDJny1nNVb8rMymOSAbbLGJs7lMq-yhf4oM$
> > 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
> >
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!O5HPWrqlPGC-qwrlP4IfT3prL6nCy0OZ_uo0iA8PjDJny1nNVb8rMymOSAbbLGJs7lMqF87GImM$
>
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Received on Fri Aug 12 2022 - 17:00:03 PDT
