Hi.
I have a problem with SHAKE ( coordinate resetting cannot be ...)
My system is a protein-ligand solvated with a cap of waters of 20 Å
(total charge of the
system is 6).
First, I have minimized it in the following way ( AMBER 7):
Minimization with Cartesian restraints
&cntrl
imin=1, maxcyc=5000,
scee=1.2, igb=0, ntb=0,
ntr=0, ibelly=0,
ntmin=1, ncyc=1000, nsnb=25, cut=10,
&end
&ewald
eedmeth=5,
&end
and then I have run a dynamics for 100 ps:
ntx=1, ntpr=100, ntwx=100, ntwv=100, ntwe=100,
ntf=2, ntc=2,
ntb=0, igb=0, cut=10, scnb=2, scee=1.2,
ibelly=0, ntr=1,
nstlim=50000, ntt=1, tautp=0.2,
dt=0.002,
&end
&wt
type='TEMP0', istep1=0, istep2=10000,
value1=0, value2=300.0,
&end
&wt
type='TEMP0', istep1=10000, istep2=50000,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&ewald
eedmeth=5,
&end
&rst
iat=0,
&end
fixed residues (away from the active center)
1000.0
RES 1 2
RES 4 6
RES 65 65
RES 68 86
RES 116 139
RES 172 172
RES 174 187
END
END
After 100 ps, the system is equilibrated ( ETOT constant, RMS
constant...)
Then, I try to run a production ( same as above) for 300 ps.
However I have a SHAKE problem.
I have seen different solutions in similar e-mails, but it doesn`t help
me:
1) VLIMIT is 20
2) The cutoff is smaller ( 10 ) than the diameter of the water cap (20 )
(same
happens if I use cutoff 9 or 8 ).
3) The problem happens 104 ps after the dynamics ( so, maybe is not a
problem
from the initial structure - I have checked it and it seems OK).
4) If I turn off the SHAKE OPTION ( although I have a cap of
WATBOX216 ), temperature raises a lot.
Could anybody help me?
Thanks in advance.
Received on Wed Aug 07 2002 - 08:13:12 PDT
