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
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed May 26 2010 - 05:00:08 PDT
