Dear Charles,
Thank you, that script does exactly what I needed!
I am still confused how to use "create_PosDiffPot" if I want to move
parts of the structure as a rigid body during the calculation. For
instance in the attached script I was anticipating the peptide to get
superimposed onto the reference at the end of minimization routine,
which does not happen.
Vitaly
On Fri, Apr 25, 2014 at 7:17 PM, Charles Schwieters
<char...@schwieters.org> wrote:
>
> Hello Vitaly--
>
>>
>> I would like to evaluate the energy of the ordered regions of the
>> calculated structure relative to the reference pdb. To do this, I have
>> been trying the following approach:
>>
>> #start
>> refRMSD = create_PosDiffPot("refRMSD","resi 6:63", pdbFile="reference.pdb")
>> minim = IVM()
>> protocol.initMinimize(minim)
>> minim.potList().append(refRMSD)
>> minim.group("resi 1:81") #move the protein as a rigid body
>> minim.run()
>> #end
>
> You might try the helper script targetRMSD:
>
> targetRMSD -diffSeq -selection "resid 6:63" reference.pdb file.pdb
>
> Hopefully, this gives you what you're looking for.
>
> Charles
>
import protocol, psfGen
from posDiffPotTools import create_PosDiffPot
from atomAction import randomizeDomainPos
from ivm import IVM
psfGen.seqToPSF("YADA", segName="A", singleChar=True)
protocol.genExtendedStructure("reference.pdb")
refRMSD = create_PosDiffPot("refRMSD","resi 1:4", pdbFile="reference.pdb")
randomizeDomainPos( "segid A", deltaPos=42 )
minim = IVM()
protocol.initMinimize(minim)
minim.potList().append(refRMSD)
minim.group("resi 1:4")
minim.run()
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