AMBER Archive (2006)

Subject: AMBER: Simulated Annealing problem...

From: sai vikram (vsaivikram_at_gmail.com)
Date: Fri Dec 29 2006 - 04:33:50 CST

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

--------------------------------------------------------------------------------------------------------------

Thanks in advance,

-Vikram

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