What compilers did you use to build Amber?
The only thing I can think is happening is that, for some strange reason,
your sander executable is not recognizing the namelists printed out by
MMPBSA.py. Can you attach the _MMPBSA_gb.mdin file here?
Another thing worth trying is to add a space before the &cntrl and the /
character at the end of that file (you can use -make-mdins to generate the
MDIN files, change them, and then use the same command-line with -use-mdins
instead of -make-mdins to use your modified copies).
Also make sure that sander passes all of the tests in the Amber test suite.
The reason igb=1, 2, and 5 work fine is because those GB models use a NAB
program to calculate the energies. In the next version of AmberTools, the
GB neck models (igb=7 and 8) will be available through nab as well.
HTH,
Jason
On Thu, Feb 7, 2013 at 8:23 PM, <psu4.uic.edu> wrote:
> Hi Amber,
>
> Thanks for the responses. After updating the latest Amber 12 and
> AmberTools 12 bugfix, we re-run igb=7 mmGBSA with mmPBSA.py. Following
> Jason's suggestion, when checking "_MMPBSA_*_gb.mdout", the error message
> is "Could not find cntrl namelist". The followings are our commands:
> Could anyone kindly point out the reason? (We haven't tried to use tleap
> or ParmEd to re-write the new topology files since the error message
> doesn't seem to correspond to bondi / mbondi3)
>
> 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.
>
> Cheers,
> Henry
>
> On Mon, Feb 4, 2013 at 4:16 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > 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
> > > > >> >
> > > > >> _______________________________________________
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> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > > _______________________________________________
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> > > > > 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)
> > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> Pin-Chih Su (Henry Su)
>
> Graduate Student
>
> Center for Pharmaceutical Biotechnology (MC 870)
>
> College of Pharmacy, University of Illinois at Chicago
>
> 900 South Ashland Avenue, Room 1052
>
> Chicago, IL 60607-7173
>
> office 312-996-5388
>
> fax 312-413-9303
> _______________________________________________
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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 Thu Feb 07 2013 - 19:30:04 PST
