Hello Charles,
Thank you for the fast response, the solution you propose suits me very well.
There is still an issue with a psfGen though: when seqToPSF is supplied with
ctermPatch='', the error message results:
Traceback (most recent call last):
File "stdin", line 1, in <module>
File "/opt/xplor-nih-2.24/python/psfGen.py", line 553, in seqToPSF
''' % (nterm,cterm,splitSeq))
UnboundLocalError: local variable 'cterm' referenced before assignment
Thank you,
Vitaly
----- Original Message -----
From: [email protected]
Date: Tuesday, January 11, 2011 10:03 am
Subject: Re: [Xplor-nih] Custom C-terminal residue
To: Vitaly Vostrikov <vvostri at uark.edu>
Cc: xplor-nih at nmr.cit.nih.gov
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> Hello Vitaly--
>
> > I am trying to make an ethanolamide C-terminal modification:
> > -N-CH2-CH2-OH. Because of the atom naming, I am making it as a
> > residue, rather than a patch. I have added an appropriate segment to
> > protein.top and one of the missing impropers to protein.par.
> >
> > The problem I ran into is that "psfGen.py" automatically patches the
> > C-terminus with a "CTER". I can work around this by setting cterm=''
> > in psfGen and also modifying the xplor.command a few lines later,
> but> I would like some permanent solution. Something similar to the
> case of
> > an acetyl group "if seq[0]=='ACE': nterm='' ", but for the last
> > residue would be ideal.
> >
>
> I'm glad you found a workaround. Here
> http://nmr.cit.nih.gov/xplor-nih/updates/2.27/
> I've posted a modified psfGen.py with seqToPSF updated to take a new
> argument, ctermPatch. If it is set to a blank string, no c-terminal
> patching will occur. Does this suit your needs?
>
> best regards--
> Charles
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