AMBER Archive (2004)

Subject: AMBER: restraints error

From: Venkata S Koppuravuri (
Date: Fri Jun 25 2004 - 12:10:35 CDT


I am trying to do a simulated annealing on a protein structure
restraining some of the residues. Everything goes fine when i dont have
any restraints, but when I add restraints using the command below

RES 122 163

i get the following error

 #simulated annealing protocol, 20 ps

     rfree: Error decoding variable 1 3 from:

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
    nstlim=40000, pencut=-0.001, nmropt=1,
    ntpr=100, ntt=1, ntwx=200,
    cut=15.0, ntb=0, vlimit=20,
    lastist = 7500000, lastrst = 7500000,
 &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' /
RES 122 126

Thanks in advance,


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