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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Received on Wed Apr 26 2006 - 06:07:06 PDT
