I am executing job in fallowing way..
----------------------------script---------------------------------------------------------------------
#! /bin/bash
module add amber:10.0
sander -O -i min_0_lam1_disch.in -o min_0_lam1_disch.out -p
ligand_0_TI.prmtop -c ligand_0_TI.inpcrd -r min_0_lam1_disch.rst
----------------------------------------------------------------------------------------------------------
please could u tel me how to use it with sander only ?
reg.
sushil
On Wed, May 26, 2010 at 1:49 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> this looks like you are not telling mutisander to use two groups. What
> does the script line that calls sander look like? It should be something
> like
>
> <system dependent mpi-commands> sander.MPI -ng 2 -groupfile <name>
>
> numgroup is not an input variable, it tell sander.MPI how many
> subprocesses to launch. The -ng 2 switch above should be all thats needed.
>
> Kind Regards,
>
> Thomas
>
> On Wed, May 26, 2010 5:54 am, Sushil Mishra wrote:
> > Hello all,
> >
> > I had gone through tutorial "Calculating Relative Binding Free Energies
> > for
> > Protein / Carbohydrate Complexes" and did same setup of my system. The
> > only
> > difference id that due to different comping facility, I cant use the same
> > was to submit jobs. When I am running the Ti calculation for ligand, it
> > 1st
> > step.when i do the minimization of ligand and discharging the atoms to be
> > disappear, I am getting error.
> >
> > I used same input files as mentioned in tutorial except 12A octahedral
> > water
> > box and 10A Ele cutoff instead of 9.
> > ########### input file ######################################
> > Discharge me-fucose atoms, lambda=0 endpoint input, charged
> > &cntrl
> > imin = 1, ntx = 1,
> > maxcyc=500,
> > ntpr = 100,
> > ntf = 2, ntc = 2,
> > ntb = 1, cut = 10.0,
> > icfe=1,clambda=0.1
> > ifsc=0
> > crgmask=''
> > scmask=''
> >
> > &end
> > #################### output error #########################
> > .
> > .
> > .
> > .
> > | MPI Timing options:
> > | profile_mpi = 0
> > numgroup must be 2 if icfe is set
> > Setting ifbox to 3 for non-orthogonal unit cell
> >
> > *** input error(s)
> >
> ------------------------------------------------------------------------------------------------
> > what may be the problem, i use icfe=1 but in do not understand numgroup,
> I
> > cant see any variable of this mane in manual too. can anyone of you
> > suggest
> > me that waats going wrong ?
> >
> > Regards
> >
> > ..sushil
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 26 2010 - 05:00:10 PDT
