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 <[email protected]>: > 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 > [email protected] > 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 [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
