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
