Hi Blanton, I remember I had the same problem, the H2' and H2'' are swapped. To fix this I made a backup of the topology file. Then I swapped the names H2' and H2''
Rerun your sequence2psf and psf2pdb scripts, et voila! When doing RNA, you don't need to bother about the H2'' anyhow. I don't know whether this screws up generation of DNA psf and pdb files. [Therefor the backup] Kind regard, Ramon van der Werf Radboud University of Nijmegen [And merry christmas, and best wishes for the new year] Quoting xplor-nih-request at nmr.cit.nih.gov: > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. seq2psf and pdb2psf (Blanton Tolbert) > 2. Re: seq2psf and pdb2psf (Charles at Schwieters.org) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Dec 2006 12:30:54 -0500 > From: "Blanton Tolbert" <btolbert at gmail.com> > Subject: [Xplor-nih] seq2psf and pdb2psf > To: xplor-nih at nmr.cit.nih.gov > Message-ID: > <b22d40e50612210930m4a5a9e59reb7f16c84972e75a at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello > > I am trying to use the pdb2psf and seq2psf utilities to generate structure > files for an RNA. Whenever I create the .psf file all H2's are called H2''s > and the amino notations are denoted HN' and HN''. I have been manually > editing the .psf file to the correct atom notation. However, I am convinced > that I am mis-executing the utilities. Can someone please provide me some > insight into the correct execution of these utilities? Thanks in advance. > > > > -- > Blanton Tolbert, Ph.D. > 8363 Tamar Drive, Apt. 841 > Columbia, MD 21045 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20061221/397e57ce/attachment-0001.html > > > ------------------------------ > > Message: 2 > Date: Thu, 21 Dec 2006 15:50:03 -0500 > From: Charles at Schwieters.org > Subject: Re: [Xplor-nih] seq2psf and pdb2psf > To: "Blanton Tolbert" <btolbert at gmail.com> > Cc: xplor-nih at nmr.cit.nih.gov, Charles at Schwieters.org > Message-ID: <19497.1166734203 at beige.cit.nih.gov> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hi Blanton-- > > > I am trying to use the pdb2psf and seq2psf utilities to generate structure > > files for an RNA. Whenever I create the .psf file all H2's are called > H2''s > > this is due to a small bug. You should be able to fix it using the -rna > flag with seq2psf. > > > and the amino notations are denoted HN' and HN''. > > this is due to explicit renaming in psfGen.py - around line 409. You can > manually remove it if you would like. In the next release, this renaming > will be made optional. > > Sorry for the confusion. > > regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> > > iD8DBQFFivN2PK2zrJwS/lYRAr7vAJ9hUMu5BchsuV5kYPa05K/AWD/NXACdE0gt > QUId+hoTJumDhpWbTNZQaj8= > =WUX/ > -----END PGP SIGNATURE----- > > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 46, Issue 6 > **************************************** >
