Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI

From: Ray Luo <rluo.uci.edu>
Date: Sat, 13 Mar 2021 18:33:34 -0800

Chuck,

Okay, can you email me your prmtop files off the list? I need to know
which atoms/atom types are new so I can add them to the pbsa
initiation code.

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 3:49 PM Chuck is Busy <chuckisbusy.gmail.com> wrote:
>
> 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
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 13 2021 - 19:00:02 PST
Custom Search