psf generation for at cyclic peptide

Dear all,

I am trying to generate a psf file for a small (13 aa) cyclic peptide  
based on the template, "eginput/PSF_generation/genCircPep.py".
However, it seems that it is not working: all HT1/HT2/HT3 and OT1/OT2  
are still present in the generated psf file and from careful reading  
of the numbers of the bond definitions in the psf-file it seems that  
there is defined a bond between resi 1 C and resi 13 N (it should be  
the oposite).
I appeared to be that the references in the patch definition should be  
swapped:

before: patch PEPT reference=-=(resid 1) reference=+=(resid 13) end
after:  patch PEPT reference=+=(resid 1) reference=-=(resid 13) end

but after this change xplor complaints about missing bond parameters:

  %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
   bond energy constant missing.
   target bond length missing.
   ATOM1: SEGId="    ",  RESId="13  ",  NAME="C   ",  CHEMical="C   "
   ATOM2: SEGId="    ",  RESId="1   ",  NAME="N   ",  CHEMical="NH3 "

I hope someone can help me figure out this problem!

best regards,

Jakob

--

-- 

Re: psf generation for at cyclic peptide

Hello Jakob--

>
> I am trying to generate a psf file for a small (13 aa) cyclic peptide
> based on the template, "eginput/PSF_generation/genCircPep.py".
> However, it seems that it is not working: all HT1/HT2/HT3 and OT1/OT2
> are still present in the generated psf file and from careful reading
> of the numbers of the bond definitions in the psf-file it seems that
> there is defined a bond between resi 1 C and resi 13 N (it should be
> the oposite).

Well, that's embarrassing. Clearly, that script was never
tested. Please find attached a working version of the script

my apologies--
Charles

--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt

#
# generate PSF and initial pdb w/ correct covalent geometry for
#

targetRMSD

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Re: targetRMSD

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Re: targetRMSD

Hello Daniel--

> Hello, I'm attempting to run the script targetRMSD on my ensemble.  I have
> had success looking at a specific seqgment, such as resid 10:20 however I
> ultimately want to use this script to look at the strands of my beta-barrel
> and as such would need to combine 8 different segments, i.e resid 10:20 AND
> resid 50:60 etc, however I cannot find a way for the script to recognize
> multiple segments.  

Keith nailed it: your selection should be something like
  resid 10:20 or resid 50:60

so the command would be something like

> % targetRMSD -seletion "resid 10:17 and name CA" avg.pdb struc*.pdb
> 

 targetRMSD -selection "(resid 10:17 or resid 50:60) and name CA" avg.pdb struc*.pdb

best regards--
Charles

--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt

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