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)
