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
> > > >> >
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > > _______________________________________________
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> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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
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Pin-Chih Su (Henry Su)
Graduate Student
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
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Received on Thu Feb 07 2013 - 17:30:03 PST
