Hi Dr Case and Dr Simmerling,
Thanks for your reply.
I am using Amber7. I did add the line as both of you have suggested
but i still get the same error. can you please advice me
Also I actually have to restrain different ranges of residues i.e.
122 to 163 (which i already have in the input file)
293 to 322
506 to 574
812 to 831
when I include them in the input file later, is it alright if I just say
as below or is there a different way
--------
restrain residues 122-163
1.0
RES 122 163
END
restrain residues 293-322
RES 293 322
END
.....and so on
------------
below is the new input file
----------------------
#simulated annealing protocol
#
#
&cntrl
nstlim=40000, pencut=-0.001, nmropt=1,
ntpr=100, ntt=1, ntwx=200,
cut=15.0, ntb=0, vlimit=20,
ntr=1,
lastist = 7500000, lastrst = 7500000,
/
&ewald
eedmeth=5,
/
&end #
&wt type='TEMP0', istep1=0,istep2=500,value1=0.,
value2=100., /
&wt type='TEMP0', istep1=500,istep2=1000,value1=100.,
value2=100., /
&wt type='TEMP0', istep1=1001,istep2=1500,value1=100.,
value2=200., /
&wt type='TEMP0', istep1=1501,istep2=2000,value1=200.,
value2=200., /
&wt type='TEMP0', istep1=2001,istep2=2500,value1=200.,
value2=300., /
&wt type='TEMP0', istep1=2501,istep2=3000,value1=300.,
value2=300., /
&wt type='TEMP0', istep1=3001,istep2=3500,value1=300.,
value2=400., /
&wt type='TEMP0', istep1=3501,istep2=4000,value1=400.,
value2=400., /
&wt type='TEMP0', istep1=4001,istep2=4500,value1=400.,
value2=500., /
&wt type='TEMP0', istep1=4501,istep2=5000,value1=500.,
value2=500., /
&wt type='TEMP0', istep1=5001,istep2=5500,value1=500.,
value2=600., /
&wt type='TEMP0', istep1=5501,istep2=10000,value1=600.,
value2=600., /
&wt type='TEMP0', istep1=10001, istep2=12000, value1=600.0,
value2=500.0, /
&wt type='TEMP0', istep1=12001, istep2=14000, value1=500.0,
value2=400.0, /
&wt type='TEMP0', istep1=14001, istep2=16000, value1=400.0,
value2=300.0, /
&wt type='TEMP0', istep1=16001, istep2=20000, value1=300.0,
value2=300.0, /
&wt type='TAUTP', istep1=0,istep2=10000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=10001,istep2=16000,value1=3.0,
value2=3.0, /
&wt type='TAUTP', istep1=16001,istep2=19000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
value2=0.05, /
&wt type='END' /
restraint residues122-163
1.0
RES 122 163
END
END
END
-----------------------------------------
Thanks,
-Venkat
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Received on Fri Jun 25 2004 - 19:53:01 PDT
