Note, igb=7 and igb=8 are different GB models that require different radius
sets than other GB models. For instance, if you run with igb=7 in the
first MMPBSA.py test, you'll get an error like:
Atom 40 has radius 0.800000000000000 outside of allowed
rang
e
of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with bondi radii.
igb=7 requires the 'bondi' radii and igb=8 requires 'mbondi3'. Unlike
other GB models, not adhering to certain criteria will cause fatal errors
(because the look-up tables used for the GB 'neck' contribution to the
effective radii impose an upper- and lower- limit on the allowable
intrinsic radii).
Look for one of these errors in the _MMPBSA_*_gb.mdout.* files. If this is
the case, you will need to regenerate your topology files with the correct
radii.
You can do this either using tleap to recreate all of your topology files,
or you can use ParmEd (xparmed.py or parmed.py) to write a new topology
file directly with the new radii.
HTH,
Jason
P.S., in some instances using other protein force fields, like ff99SBildn,
will result in the same error for igb=8 even when you use mbondi3. In this
case, you need to use ParmEd to change the radii of all C2 (or C3) atoms
from 2.2 to 1.7. So a command like this:
change RADII .%C2,C3 1.7
will do the trick.
On Mon, Feb 4, 2013 at 4:47 PM, <psu4.uic.edu> wrote:
> Hi Amber,
>
> We run on Lonestar, Amber 12 and AmberTools 12. The bugfix is bugfix.13
> for Amber 12 and bugfix.30 for AmberTools 12. When we installed it, we try
> the test cases. We have also run a lot of MMGBSA (igb=1,2,5) and MMPBSA
> using MMPBSA.py without any error. Because the Amber manuals only say
> " Selecting 7 or 8 will require sander", we guess we might need more flags
> to enable igb=7 or 8?
>
> We will update the latest bugfix for Amber12 and AmberTools 12 to see if
> it helps.
>
> Cheers,
> Henry
>
> On Mon, Feb 4, 2013 at 9:46 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > What version of Amber are you using and what bugfixes have been
> > applied? Also, do all of your test cases pass (particularly the MMPBSA
> > tests)? Have you tried running serial MMPBSA as well?
> >
> > -Dan
> >
> > On Sun, Feb 3, 2013 at 2:55 PM, <psu4.uic.edu> wrote:
> > > Dear Amber,
> > >
> > > Here is the more detailed input:
> > >
> > > ibrun MMPBSA.py.MPI -O -i mmgbsa.in -o result.dat -sp
> > > protein_ligand_12A.prmtop -cp protein_ligand.prmtop -rp protein.prmtop
> > -lp
> > > ligand.prmtop -y protein_ligand_12A.mdcrd
> > >
> > > For mmgbsa.in
> > >
> > > Input file for running mmPBSA
> > > &general
> > > keep_files=2,use_sander=1,
> > > /
> > > &gb
> > > igb=7, saltcon=0.100
> > > /
> > >
> > > The issue only occurs if I use igb=7 or 8. igb=1,2,5 are fine.
> > >
> > > Thanks.
> > >
> > > Cheers,
> > > Henry
> > >
> > > On Sat, Feb 2, 2013 at 9:08 PM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > >> That's your entire input?
> > >> On Feb 2, 2013 6:50 PM, <psu4.uic.edu> wrote:
> > >>
> > >> > Dear Amber,
> > >> >
> > >> > When we use igb=7 or 8, there is an error message:
> > >> > CalcError: "pathway" failed with prmtop "protein".prmtop.
> > >> > error occured on rank "number".
> > >> >
> > >> > However, we don't encounter the same issue in igb=1 or 2 or 5.
> > >> >
> > >> > Here is the input file for igb=7 & 8
> > >> >
> > >> >
> > >> >
> > >> > &general
> > >> > keep_files=2, use_sander=1,
> > >> > /
> > >> > &gb
> > >> > igb=7, saltcon=0.100,
> > >> > /
> > >> >
> > >> >
> > >> >
> > >> > Could someone help out? Thanks.
> > >> >
> > >> > Cheers,
> > >> > Henry
> > >> > _______________________________________________
> > >> > 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
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 04 2013 - 14:30:02 PST
