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
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> >>
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> > 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)
>
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Received on Mon Feb 04 2013 - 14:00:02 PST
