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
