which amber version is it? amber8 can use different
format for restraint mask.
also, you might need a title and a force constant for your
restraint section (right before the RES line) and an additional END.
title line for restrained atom definition
5.0
RES 122 163
END
END
carlos
----- Original Message -----
From: "Venkata S Koppuravuri" <kvsuneel.linus.bmb.wright.edu>
To: "amber group" <amber.scripps.edu>
Sent: Friday, June 25, 2004 1:10 PM
Subject: AMBER: restraints error
>
> Hi,
>
> 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
> END
> ---------
>
> i get the following error
>
> ---------------------------------
> ----- READING GROUP 1; TITLE:
> #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
> #
> #
> &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' /
> RES 122 126
> END
> END
> ------------------------------
>
>
> Thanks in advance,
>
> -Venkat
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jun 25 2004 - 18:53:00 PDT
