Hi,
I am trying to do a simulated annealing on a protein structure restraining
Restrain 2 to 20 residues
50.0
Restrain the CA atom of first residue strongly
1000.0
Before this particular run i carried out a minimization with restrains as
mentioned above.
I wish my system should be at constant pressure 200.0 .
*******************************************************************************
Error:
too many values for NAMELIST variable
The Out Put file stopped at:
| peek_ewald_inpcrd: Box info found
Largest sphere to fit in unit cell has radius = 75.000
*******************************************************************************
I have tried to search in google and read the messages posted previously
by others, but they were not of much help.
$ Can someone please advice me here. below is my input file
--------------------------------------------------------------------------------------------------------------------
#simulated annealing protocol
&cntrl
imin = 0, ntx =1, irest = 0,
ntpr = 100, ntwx = 0, ntwe = 0,
ntc = 2, ntf = 2,
nstlim = 25000, dt =0.002,
nmropt = 1, ntt =1, tautp =2.0,
ntb = 2, ntp = 1, taup = 0.2, pres0 = 200.0,
ntr = 1,cut = 10.0,iwrap=1
&end
#
# from steps 0 to 5000:raise temperature 10->100K
# from steps 5001 to 10000:equilibrate under 100K
# from steps 10001 to 15000:raise temperature 100->200K
# from steps 15001 to 20000:equilibrate under 200K
# from steps 20001 to 25000:raise temperature 200->300K
#
&wt type='TEMP0', istep1=0,istep2=5000, value1=10.,
value2=100., &end
&wt type='TEMP0', istep1=5001,istep2=10000, value1=100.,
value2=100., &end
&wt type='TEMP0', istep1=10001,istep2=15000, value1=100.,
value2=200., &end
&wt type='TEMP0', istep1=15001,istep2=20000, value1=200.,
value2=200., &end
&wt type='TEMP0', istep1=20001,istep2=25000, value1=200.,
value2=300., &end
&wt type='END'
Restrain the heavy atoms
50.0
RES 2 20
END
Restrain the CA atom of first residue strongly
1000.0
FIND
* CA * *
SEARCH
RES 1
END
END
Amber Version : 9
Operating System : Linux
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Thanks in advance,
-Vikram
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Received on Sun Dec 31 2006 - 06:07:36 PST
