Re: Fwd: Majordomo results

From: farzad kiani (farzad_kiani1364_at_yahoo.com)
Date: Wed Jan 01 2014 - 14:57:29 CST

" ../common/ap9_2_ws.psf" what is this???????!!!!!!!!! you have been set incorrect directories for your files. set them correctly On Wednesday, January 1, 2014 2:55 PM, Faezeh Mottaghitalab <faezeh.mt258_at_gmail.com> wrote: Hello I'm trying to simulate Bacteriorhodopsin with the NAMD 2.9 in unix. first of all i have been omitted the retinal group of the protein from the pdb file and i have gain the files for the 1-2 sphere, 1-3 box  and 1-4 gbis ( to explain better i preferred to write the steps same as tutorial file 'ubq').  i'm now in the 2-4 temp step and the problem is i get error 'segmentation fault' in this step and can't understand what is the problem. first i guess that maybe the dcd , vel ,xsc files haven't been created correctly but i have tested again and again different namd-tutorial-files and get the same error (segmentation fault)! the pdb id of the bacteritodopsin that i'm using is : 1AP9 and  here is my configuration file : ############################################################# ## JOB DESCRIPTION                                         ## ############################################################# # Equilibration of Ubiquitin in a Water Sphere # Use for calculating temperature fluctuations # WARNING: DOES NOT SAVE DCD (and normally you need it) ############################################################# ## ADJUSTABLE PARAMETERS                                   ## ############################################################# structure          ../common/ap9_2_ws.psf coordinates        ../common/ap9_2_ws.pdb set temperature    310 set outputname     ap9_2-nve # Continuing a job from the restart files if {1} { set inputname      ../1-2-sphere/ap9_2_ws_eq binCoordinates     $inputname.restart.coor binVelocities      $inputname.restart.vel  ;# remove the "temperature" entry if you use this! extendedSystem     $inputname.restart.xsc }  firsttimestep      0 ############################################################# ## SIMULATION PARAMETERS                                   ## ############################################################# # Input paraTypeCharmm    on parameters          ./common/par_all27_prot_lipid.inp  #temperature         $temperature # Force-Field Parameters exclude             scaled1-4 1-4scaling          1.0 cutoff              12.0 switching           on switchdist          10.0 pairlistdist        13.5 # Integrator Parameters timestep            2.0  ;# 2fs/step rigidBonds          all  ;# needed for 2fs steps nonbondedFreq       1 fullElectFrequency  2   stepspercycle       10 # Constant Temperature Control if { 0 } { langevin            on    ;# do langevin dynamics langevinDamping     5     ;# damping coefficient (gamma) of 5/ps langevinTemp        $temperature langevinHydrogen    off    ;# don't couple langevin bath to hydrogens } # Output outputName          $outputname #restartfreq         50     ;# 500steps = every 1ps #dcdfreq             50 outputEnergies      50 outputPressure      50 ############################################################# ## EXTRA PARAMETERS                                        ## ############################################################# # Spherical boundary conditions sphericalBC         on sphericalBCcenter   16.626047134399414, 39.246639251708984, 6.797718524932861 sphericalBCr1       26.0 sphericalBCk1       10 sphericalBCexp1     2 ############################################################# ## EXECUTION SCRIPT                                        ## ############################################################# # Minimization # minimize            900 # reinitvels          $temperature run 5000 ;# 1000ps thanks in advance, faezeh ---------- Forwarded message ---------- From: <majordomo_at_ks.uiuc.edu> Date: Wed, Jan 1, 2014 at 1:32 PM Subject: Majordomo results To: faezeh.mt258_at_gmail.com -- >>>> --047d7b41baea7d246804eee5c608 >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>>  subscribe namd-l **** Address already subscribed to namd-l >>>> >>>> --047d7b41baea7d246804eee5c608 >>>> Content-Type: text/html; charset=ISO-8859-1 >>>> >>>> <div dir="ltr"><pre style="font-size:large;color:rgb(0,0,0);line-height:16px"> subscribe namd-l</pre></div> >>>> >>>> --047d7b41baea7d246804eee5c608--

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