It seems you do not load the (correct) topology file for your residue. I could notdetect the topology file to be loaded in the script you send around (something like "topology @toph19.chromo" in the beginning of the script).
Best, Andre On 13 September 2011 18:00, <xplor-nih-request at nmr.cit.nih.gov> wrote: > 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. using chromophore residues from toph19.chromo to generate psf > (Jakob Toudahl Nielsen) > 2. Re: using chromophore residues from toph19.chromo to generate > psf (Jakob Toudahl Nielsen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 13 Sep 2011 11:40:51 +0200 > From: Jakob Toudahl Nielsen <jtn at chem.au.dk> > Subject: [Xplor-nih] using chromophore residues from toph19.chromo to > generate psf > To: xplor-nih at nmr.cit.nih.gov > Message-ID: <20110913114051.91995m2bnj9d48ir at webmail.nfit.au.dk> > Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" > > Dear all, > > I would like to calculate a structure containing a bacteriochlorophyll > a (bchla) ligand. I have found what I believe is a defintion of > parameters for this ligand in the file "toph19.chromo". In this file I > would think that the ligand parameters are wrapped up in the > "RESIdue BCL" and following statements > > As the first step I tried to generate the psf file from sequence > templates using the BCL residue for the ligand. A problem occurs when > I try loading the parameters, maybe I do in the wrong place or > context, hope your can help me, here is my test script: > > parameter @TOPPAR:protein.par @TOPPAR:toph19.chromo end > > segment > name="A " > SETUP=TRUE > chain > @TOPPAR:toph11.pep > sequence > HIS BCL > end > end > end > > write psf output=test.psf end > > This leads to parsing errors regardsless of if I put the loading of > BCL parameters within the chain block. The parsing errors seams to be > related to the AUTOGENERATE keyword, which is not recognized, in the > toph19.chromo. Here is that top part of the content of toph19.chromo: > > remarks toph19.chromo (CHROMOPHORE RESIDUE'S ) > remarks ================================================ > remarks Authors: Herbert Treutlein and Axel Brunger > remarks warning: this file is under development > > set echo=false end > > AUTOGENERATE ANGLES=TRUE END {* but see the two omitted angles below > *} > {*============================ ==================================== > *} > > {* protein default masses *} > MASS H 1.00800! hydrogen which can h-bond to neutral atom > MASS HC 1.00800! ="= ="= ="= to charged atom > > Hope you can help to point out where I am wrong. > > > Furthermore, the bchla in our structure is bound to a histidine. Would > it be advisable to use the PBCL patch? That means that I use PBCL in > place of HIS and BCL? > > > best regards, > > Jakob > > I am using xplor-nih 2.26 > > -- > Jakob Toudahl Nielsen, post doc > Laboratory for Biomolecular NMR Spectroscopy > inSPIN, Center for Insoluble Protein Structures > Department of Chemistry, University of Aarhus > Langelandsgade 140, DK-8000 Aarhus C, Denmark > Phone: +458942 5528 or +452993 8502 (cell) > > > ------------------------------ > > Message: 2 > Date: Tue, 13 Sep 2011 14:30:01 +0200 > From: Jakob Toudahl Nielsen <jtn at chem.au.dk> > Subject: Re: [Xplor-nih] using chromophore residues from toph19.chromo > to generate psf > To: xplor-nih at nmr.cit.nih.gov > Message-ID: <20110913143001.11585fpr5telv5xl at webmail.nfit.au.dk> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear all, > > sory, I realize that I need the "param19.chromo" as the parameter > file. However, this time I still get errors, it seams that the BCL > residue is not recognized. Here is output from the psf generation, > which fails to generate parameters for BCL. > > ... > CHAIN>sequence > SEQUENCE>HIS BCL > MAPIC: Atom numbers being modified > %GENRES-ERR: residue BCL not found in topology file > %PATCH-ERR: bond -C +N not found > %PATCH-ERR: angle -CA -C +N not found > %PATCH-ERR: angle -O -C +N not found > ... more PATCH-ERRs... > > hope that someone can help to find out what I do wrong. > > best regards, > > Jakob > > > > Citing Jakob Toudahl Nielsen <jtn at chem.au.dk>: > > > Dear all, > > > > I would like to calculate a structure containing a bacteriochlorophyll > > a (bchla) ligand. I have found what I believe is a defintion of > > parameters for this ligand in the file "toph19.chromo". In this file I > > would think that the ligand parameters are wrapped up in the > > "RESIdue BCL" and following statements > > > > As the first step I tried to generate the psf file from sequence > > templates using the BCL residue for the ligand. A problem occurs when > > I try loading the parameters, maybe I do in the wrong place or > > context, hope your can help me, here is my test script: > > > > parameter @TOPPAR:protein.par @TOPPAR:toph19.chromo end > > > > segment > > name="A " > > SETUP=TRUE > > chain > > @TOPPAR:toph11.pep > > sequence > > HIS BCL > > end > > end > > end > > > > write psf output=test.psf end > > > > This leads to parsing errors regardsless of if I put the loading of > > BCL parameters within the chain block. The parsing errors seams to be > > related to the AUTOGENERATE keyword, which is not recognized, in the > > toph19.chromo. Here is that top part of the content of toph19.chromo: > > > > remarks toph19.chromo (CHROMOPHORE RESIDUE'S ) > > remarks ================================================ > > remarks Authors: Herbert Treutlein and Axel Brunger > > remarks warning: this file is under development > > > > set echo=false end > > > > AUTOGENERATE ANGLES=TRUE END {* but see the two omitted > > angles below *} > > {*============================ > > ==================================== *} > > > > {* protein default masses *} > > MASS H 1.00800! hydrogen which can h-bond to neutral atom > > MASS HC 1.00800! ="= ="= ="= to charged atom > > > > Hope you can help to point out where I am wrong. > > > > > > Furthermore, the bchla in our structure is bound to a histidine. Would > > it be advisable to use the PBCL patch? That means that I use PBCL in > > place of HIS and BCL? > > > > > > best regards, > > > > Jakob > > > > I am using xplor-nih 2.26 > > > > -- > > Jakob Toudahl Nielsen, post doc > > Laboratory for Biomolecular NMR Spectroscopy > > inSPIN, Center for Insoluble Protein Structures > > Department of Chemistry, University of Aarhus > > Langelandsgade 140, DK-8000 Aarhus C, Denmark > > Phone: +458942 5528 or +452993 8502 (cell) > > _______________________________________________ > > Xplor-nih mailing list > > Xplor-nih at nmr.cit.nih.gov > > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > > > > -- > Jakob Toudahl Nielsen, post doc > Laboratory for Biomolecular NMR Spectroscopy > inSPIN, Center for Insoluble Protein Structures > Department of Chemistry, University of Aarhus > Langelandsgade 140, DK-8000 Aarhus C, Denmark > Phone: +458942 5528 or +452993 8502 (cell) > > > ------------------------------ > > _______________________________________________ > 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 103, Issue 4 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... 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