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)
