Dear All,
In my protein two residues were missing which i added using biopolymer
module of SYBYL.After neutralising and adding explicit solvent, when i am
minimizing only solvent job is ok but while minimising the whole protein the
last coordinates in my restart file are 0.00. If i am submitting the job by
using the same restart file the job is not running, however after deleting
the last zeroes from restart file the further job is running. But i am not
able to achieve stable structure in equilibration step even after 1.5ns
run.my input files are as,
min1:
initial minimization for only solvent and ios
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 500,
ntb = 1,
ntr = 1,
ntr = 1,
restraint_wt = 500.0
restraintmask = :1-335,
cut = 10.0
/
min2:
initial minimization whole system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 10.0
/
equil: heat full-pro
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Kindly suggest me that whether non-stabilisation in equilibration step is
due to this restart file error and how can i overcome.
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Received on Wed Oct 13 2010 - 11:00:08 PDT
