Hi,
you must use the parallel version, sander.MPI. There are no TI facilities
in regular sander.
Kind Regards,
Thomas
On Wed, May 26, 2010 7:55 am, Sushil Mishra wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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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Received on Wed May 26 2010 - 06:30:04 PDT
