Hi Ray,
I have tried this before and I get an error/PB Bomb:
PB Bomb in pb_aaradi(): No radius assigned for atom 1 N NH3
I attached the full .out file as well.
On Sat, Mar 13, 2021 at 6:32 PM Ray Luo <rluo.uci.edu> wrote:
> Hi Chuck,
>
> If you can run your amber MD simulations and your only issue is lack
> of radii for pbsa, how about setting radiopt=1 in the mmpbsa input so
> pbsa can set the radii for you?
>
> However, the caveat is that there could be newer atom types defined
> if newer protein force fields are used. Hopefully these atom types
> have been added to pbsa in newer Amber releases.
>
> 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 Sat, Mar 13, 2021 at 3:05 PM Chuck is Busy <chuckisbusy.gmail.com>
> wrote:
> >
> > So...CHARMM-GUI converts the structure to the Amber format with prmtop
> and
> > rst7. I used those files to run my simulation, and I used that same
> prmtop
> > file to create my complex, receptor, and ligand prmtop file with cpptraj.
> > At the time, I didn't realize that my CHARMM-GUI prmtop file doesn't have
> > any radii defined. After I create my 3 topology files to run sander, I
> get
> > that error because none of those files have a radii mentioned. Then I go
> > back and set mbondi as my radii for my 3 topology files and I guess I'm
> > overestimating my values.
> >
> > If my simulation was run without defining a radii, what radii or what
> > values can I set for my 3 topology files to get reasonable values with
> > sander?
> > Or can I use cpptraj to trajout a trajectory with new radii?
> >
> >
> > On Sat, Mar 13, 2021 at 5:08 PM David A Case <david.case.rutgers.edu>
> wrote:
> >
> > > On Sat, Mar 13, 2021, Chuck is Busy wrote:
> > > >
> > > >Do you have any better insight on how I can define the 1-4 EEL and
> 1-4 VDW
> > > >scale factors so I can run PBSA calculations on my protein system? The
> > > >protein membrane system was built in CHARMM-GUI and the CHARMM force
> field
> > > >but simulated using AMBER.
> > >
> > > If you ran the simulation with Amber, you have prmtop files with the
> > > appropriate values of SCEE and SCNB in them (as highlighted here from
> your
> > > output):
> > >
> > > >| Note: 1-4 EEL scale factors are being read from the topology file.
> > > >| Note: 1-4 VDW scale factors are being read from the topology file.
> > >
> > > >If I set my radii to mbondi with parmed.py and set scnb and scee to
> 1. I
> > > >can get MMPBSA to run this way using sander, but after doing my
> > > >subtractions I get extremely positive values like 1200 to 1700.
> Wondering
> > > >if there is a more appropriate way to do this..
> > >
> > > Why are you changing scnb and scee with parmed? Setting the radii
> makes
> > > sense to me, but I'm not sure why you want to change scnb and scee.
> > >
> > > ...hoping the others on the list will correct any mistakes above.
> > >
> > > ....dac
> > >
> > >
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Received on Sat Mar 13 2021 - 16:00:02 PST
