Problem solved. The numbering of the residues was shifted. Strangely that doesnt give you an error in the process but messes up the terminus.
Thanks for support. -------- Original-Nachricht -------- > Datum: Tue, 21 Dec 2010 14:26:30 +0000 > Von: "David A. Horita" <dhorita at wfubmc.edu> > An: "xplor-nih at nmr.cit.nih.gov" <xplor-nih at nmr.cit.nih.gov> > Betreff: Re: [Xplor-nih] (no subject) > Are you sure you've patched your protein correctly? I don't think that > your seq2psf command protects the N-terminus (hence errors about HT1-3). You > may have N-acetyl coordinates with a free N-terminal parameter set. > > Regards, > David > > > ----------------------------- > David A. Horita, Ph.D. > Department of Biochemistry > Wake Forest University School of Medicine > Winston-Salem, NC 27157-1016 > Tel: 336 713-4194 > Fax: 336 716-7671 > email: dhorita at wfubmc.edu > web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm > > -----Original Message----- > From: xplor-nih-bounces at nmr.cit.nih.gov > [mailto:xplor-nih-bounces at nmr.cit.nih.gov] On Behalf Of Daniel Schaal > Sent: Tuesday, December 21, 2010 6:44 AM > To: xplor-nih at nmr.cit.nih.gov > Subject: Re: [Xplor-nih] (no subject) > > Ok now i managed to create the template, but there are 3 protons (HT1,2,3) > which are randomly in space. Are they supposed to belong to the N-terminal > capping? > I ran a calculation and the protons do not seem to disturb but they are > spreaded over a wide space. I can delete them from the template. Why are they > created and how do i get rid of them in the psf file. > > Cheers > > > -------- Original-Nachricht -------- > > Datum: Tue, 21 Dec 2010 09:37:31 +0100 > > Von: Daniel Schaal <spqrtitus at gmx.de> > > An: xplor-nih at nmr.cit.nih.gov > > Betreff: Re: [Xplor-nih] (no subject) > > > Well it is on a Mac. > > > > I tried the protein.par and protein-2.0.par. > > > > When i write the .psf file there is following issue: > > > > > > ~/xplor/xplor-nih-2.26/bin] schaal% ./seq2psf -protein -amidate_cterm > > -startresid 143 protein01.seq > > %PATCH-ERR: atom +N not found > > %PATCH-ERR: atom +HN not found > > %PATCH-ERR: bond +HT1 +N not found > > %PATCH-ERR: bond +HT2 +N not found > > %PATCH-ERR: bond +HT3 +N not found > > %PATCH-ERR: angle +HT1 +N +HT2 not found > > %PATCH-ERR: angle +HT2 +N +HT3 not found > > %PATCH-ERR: angle +HT2 +N +CA not found > > %PATCH-ERR: angle +HT1 +N +HT3 not found > > %PATCH-ERR: angle +HT1 +N +CA not found > > %PATCH-ERR: angle +HT3 +N +CA not found > > > > but the file is made. > > Does this link to the other "missing" parameters? > > > > -------- Original-Nachricht -------- > > > Datum: Mon, 20 Dec 2010 10:56:58 -0500 > > > Von: Charles at Schwieters.org > > > An: Daniel Schaal <spqrtitus at gmx.de> > > > CC: xplor-nih at nmr.cit.nih.gov > > > Betreff: Re: [Xplor-nih] (no subject) > > > > > -----BEGIN PGP SIGNED MESSAGE----- > > > Hash: SHA1 > > > > > > > > > Hello Daniel-- > > > > > > > > > > > i try to run simulated annealing with a n- and c-terminal > > > > protected peptide. > > > > I managed to get the .psf file but the template generation is > > > > aborting with the following error. > > > > > > > > > > > > %CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%% > > > > improper energy constant missing. > > > > target improper value missing. > > > > periodicity missing. > > > > ATOM1: SEGId=" ", RESId="143 ", NAME="HA1 ", CHEMical="HA " > > > > ATOM2: SEGId=" ", RESId="143 ", NAME="HA2 ", CHEMical="HA " > > > > ATOM3: SEGId=" ", RESId="143 ", NAME="C ", CHEMical="C " > > > > ATOM4: SEGId=" ", RESId="143 ", NAME="HA3 ", CHEMical="HA " > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > %CODIMP-ERR: program will be aborted. > > > > > > > > So i guess these data are missing in some file. > > > > This is the ACE group. I did see it listed in the protein.top > > > > file, so why do the parameter miss ? > > > > > > are you using toppar/protein.par for the parameters? The parameters > > > for this improper is defined in that file. > > > > > > best regards-- > > > Charles > > > -----BEGIN PGP SIGNATURE----- > > > Version: GnuPG v1.4.10 (GNU/Linux) > > > Comment: Processed by Mailcrypt 3.5.9 > > <http://mailcrypt.sourceforge.net/> > > > > > > iEYEARECAAYFAk0PfMoACgkQPK2zrJwS/lbVCACfTHxVeqm95tHpiavMd6ZSgapu > > > Rd8An1CTJwFDlgLrT5X1Y7aymJb76Bgl > > > =CRxy > > > -----END PGP SIGNATURE----- > > > > -- > > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt auch mit gratis > > Notebook-Flat! http://portal.gmx.net/de/go/dsl > > _______________________________________________ > > Xplor-nih mailing list > > Xplor-nih at nmr.cit.nih.gov > > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt auch mit gratis > Notebook-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail
