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Hello Charlie--
>
> I am currently running Xplor-NIH 2.27 compiled on a linux machine. I
> am trying to run calculations on a RNA duplex but when I try and make
> the .psf and .pdb files they have an H2'' in them which is not correct
> for RNA. Is there a way to run the mkpsf file and have it create the
> 2' OH group instead of an H2''?
>
Not sure which script you're using. You can generate a psf using
seq2psf using the -rna option, or work from
eginput/PSFgeneration/genExtendedDNA.py and change seqType from dna to
rna. For example:
xplor.parseArguments() # check for typos on the command-line
simWorld.setRandomSeed(3421) #set random seed
import protocol
from psfGen import seqToPSF
seqToPSF('RNA.seq',seqType='rna') # place 3-character sequence in RNA.seq
protocol.genExtendedStructure("new.pdb",verbose=1)
xplor.command("write psf output=new.psf end")
best regards--
Charles
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