AMBER Archive (2004)

Subject: Re: AMBER: restraints error

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Jun 25 2004 - 13:19:34 CDT


check the amber manual on this, I think it explains it or gives
examples. no new title netween lines.

title
1.0
RES X X
RES X X
END
END

----- Original Message -----
From: "Venkata S Koppuravuri" <kvsuneel_at_linus.bmb.wright.edu>
To: <amber_at_scripps.edu>
Sent: Friday, June 25, 2004 2:11 PM
Subject: Re: AMBER: restraints error

> 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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