Hello,
It is normally placed just after the &cntrl ----&end
for example
Group input for restrained Residues - AA-162
10.0 !(force constant for restraint)
RES 162
END
Group input for restrained Residues 200-210
10.0 !(force constant for restraint)
RES 200 210
END
END
Wherever you put please check the output file . It shoud give the
informations on how many atoms has been put under restrained. If you do not
find this informations, it is wrong.
Good luck,
JIten
----- Original Message -----
From: <anshul.imtech.res.in>
To: "amber mail reflector" <amber.scripps.edu>
Sent: Thursday, June 03, 2004 11:12 PM
Subject: AMBER: simulated anealling
> Hi all,
> I am trying to do simulated anealling and had written earlier also about
> the problems i faced in the same process. Previously I was told by Dac
> that I should place the group information regarding the restraints after
> the cntrl section but I was not able to run the process properly as the
> groups were not read. So itried to run the same process by keeping the
> group information in the begining followed by cntrl section and then
> eedmeth=5 flag. this time it is running fine.
> 1 it reads the group nformation properly
> 2. sets the dielectric to distance dependent
>
> i want to know if this is all right or not. Any comments regarding
> theis process will be helpful. Here is my input file for the
> same process
>
>
> Group input for restrained atoms (A1-A166)
> 2
> RES 1 167 END
> Group input for restrained atoms (A182-A276)
> 2
> RES 182 276
> END
> END
>
> &cntrl
> imin=0, cut=30, nstlim=90000, ntt=1, ntx=1, irest=0,
> ntpr=500, ntwx=500, ntwe=500, tempi=10,
> ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,
> &end
>
> &ewald
> eedmeth=5,
> &end
>
> &wt type='TEMP0', istep1=0,istep2=50000,value1=10.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=50001,istep2=60000,value1=500.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=60001,istep2=70000,value1=500.0,
> value2=300.0, &end
> &wt type='TEMP0', istep1=70001,istep2=90000,value1=300.0,
> value2=300.0, &end
> &wt type='TAUTP', istep1=0,istep2=50000,value1=1.0,
> value2=1.0 &end
> &wt type='TAUTP', istep1=50001,istep2=60000,value1=0.5,
> value2=0.5, &end
> &wt type='TAUTP', istep1=60001,istep2=70000,value1=0.5,
> value2=0.5 &end
> &wt type='TAUTP', istep1=70001,istep2=90000,value1=0.2,
> value2=0.2 &end
> &wt type='END' &end
>
>
>
> With regards,
> Anshul
>
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Received on Thu Jun 03 2004 - 05:53:00 PDT
