AMBER Archive (2006)

Subject: AMBER: LES copies

From: Claudia Steinert (fluffybelly_at_gmx.de)
Date: Mon Apr 24 2006 - 03:28:06 CDT

Hello Amber Users,
i tried to copy a region in my protein with amber LES.
My protein consists of 642 atoms (46 aa) and i wanted to copy atom no 230
to 346 five times.
I used the following input for addles:
 
file rprm name=(crm_wat.top) read
file rcrd name=(crm_min_wat.crd) read
file wprm name=(crm_addles_wat.top) wovr
file wcrd name=(crm_addles_wat.crd) wovr
action
spac numc=5 pick #prt 230 346 done
*EOD
 
and this one for sander_les:
 
# md using sander heatup tempi=0 isotrop press scaling
 &cntrl
 irest=0, ntx=1, imin=0, nstlim=150000,
 nsnb=25, tempi=0.0, temp0=300.0, scee=1.2,
 ntt=1, tautp=1.0, dt=0.001,
 ntc=2, ntf=2, cut=10.0,
 ntb=2, ntp=1, nmropt=0,
 ntpr=100, ntwe=100, ntwx=100,
 ntr=0,
 /
 
after using addles i created a pdb file and checked, that the copies were
actually made.
  
as i tried to extract the different copies after sander_les in moilview,
there was no difference between the resulting trajectories and
structures.
 
even as i increased the temperature in sander_les the trajectories
remained identical.
 
does anybody know, where the problem is?
    
thank you in advance,
claudia
      
      
  
  

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