Dear Doc,
Yes, I found the erro in the mdout files.Thanks very much. The progam
worked now.
Now, if the V0 state is a protein-ligand complex with one crystal water
(that is PLW(sol) ), and the V1 is a protein-ligand complex with the water
removed (that is PL(sol) + W(g) ). case one
if the V0 state is a solution water (that is W(sol) ), and the V1 is a gas
water (that is W(g) ). case two
how can I could apply the softcore potentials method to deal with these two
situation.
my steps are listed as follows. I use the double decoupling method to
divide each case into two steps by removing the electrostatic interaction
followed by removing vdw.
case one:
step1 (remove charge) step2 (remove
vdw)
V0 PLW(sol).top PLW(sol).top
icfe=1, ifsc=0 icfe=1,
ifsc=1
crgmask='' crgmask='WAT'
scmask='' scmask=''
V1 PLW(sol).top PL(sol).top
icfe=1, ifsc=0 icfe=1, ifsc=0
crgmask='WAT' crgmask=''
scmask='' scmask=''
case two:
step1 step2
V0 W(sol).top W(sol).top
icfe=1, ifsc=0 icfe=1,
ifsc=1
crgmask='' crgmask='WAT'
scmask='' scmask=''
V1 W(sol).top W(sol)-1.top
(remove one water)
icfe=1, ifsc=0 icfe=1, ifsc=0
crgmask='WAT' crgmask=''
scmask='' scmask=''
Is this right?
On Tue, Oct 1, 2013 at 12:07 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Sep 30, 2013 at 7:18 AM, 冉挺 <rantingjing0445019.gmail.com> wrote:
> > [cli_0]: aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > [cli_2]: aborting job:
>
> Where any output files produced (mdout, the '-o' file in particular)?
> Were there any error messages in those files? Also, what version of
> Amber are you using and what bugfixes have been applied?
>
> -Dan
>
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> > rank 0 in job 230 localhost_39799 caused collective abort of all ranks
> > exit status of rank 0: return code 1
> >>>
> > I used 4 cpus to run sander.MPI
> >
> >
> > On Mon, Sep 30, 2013 at 8:01 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Mon, Sep 30, 2013, 冉挺 wrote:
> >>
> >> > I read the tutorial that's "Thermodynamic Integration using soft
> >> core
> >> > potentials
> >>
> >> > I want to modeling the water contribution to the ligand-binding
> affinity
> >> by
> >> > the double decoupling method.
> >>
> >> It's not clear what you mean by the "water contribution to the ligand
> >> binding
> >> affinity". A "standard" simulation of the ligand binding free energy
> will
> >> automatically include the effects of the solvent.
> >>
> >> > I wonder if the icfe parameter should be set from minimization
> >> > mdin to equilibrium mdin
> >>
> >> You would ordinarily use the same icfe value at all steps. Note that
> >> minimization is often not needed.
> >>
> >> > if the water should be constraint at the
> >> > binding site by a constraint force as described in the literature
> >>
> >> You would ordinarily not constraint solvent molecules. But note that it
> >> may
> >> take a long time to equilibrate if there are trapped waters.
> >>
> >> > As well, I cannot use the pmemd method to run Thermodynamic
> Integration
> >>
> >> This is correct; the next release of pmemd will have this feature.
> >>
> >> > My command is "sander -ng 2 -groupfiles 《Mygroupfiles》"
> >> > the erro is "mdfil: Error unknown flag: -ng" but the recommended
> >> > parameters include the -ng flag. I used amber10.
> >>
> >> You must use sander.MPI (not sander), and the corresponding mpirun
> command
> >> to
> >> carry out thermodynamic integration calculations.
> >>
> >> Since you seem to be very new to this, be sure to get familiar with
> small
> >> and
> >> "easy" transformations before attempting something difficult.
> >>
> >> ...good luck...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > PhD Ting Ran
> >
> > CPU(CHINA PHARMACEUTICAL UNIVERSITY)
> > Molecular-Design & Drug-Discovery Lab
> > Laboratory Building A212
> > 639 Longmian Avenue
> > Nanjing, 210009
> > P.R.China
> > _______________________________________________
> > 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) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design & Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Tue Oct 01 2013 - 02:30:03 PDT
