Multiple Input Files for CNS

Paul Hubbard phubbard at POST.ITS.MCW.EDU
Wed Dec 16 12:10:55 EST 1998


Hi,

I'm sure this is a really easy question to answer, but I'm having trouble
reading in muliple topology and parameter files in CNS. I have 3 different
prosthetic groups, and have placed them in the relevant input parts of the
example generate script. However none of these files are read in (or at
least the toplogy and parameter files aren't). I have tried placing them
elsewhere (i.e., one in the ligand and one in the carbohydrate input
sections) but this causes SA to crash (any ideas why?). Below is part of
the generate script I've been using. Can anyone please tell me what I'm
doing wrong?

Thanks.

Paul Hubbard (Graduate Student).

{========================prosthetic group files===========================}

{* prosthetic group coordinate file *}
{===>} prost_coordinate_infile_1="fmn.pdb";
{===>} prost_coordinate_infile_2="fad.pdb":
{===>} prost_coordinate_infile_3="nap.pdb";

{* rename segid *}
{+ choice: true false +}
{===>} prost_rename_1=false;
{===>} prost_rename_2=false;
{===>} prost_rename_3=false;

{* new segid *}
{===>} prost_segid_1="";
{===>} prost_segid_2="";
{===>} prost_segid_3="";

{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} prost_convert_1=false;
{===>} prost_convert_2=false;
{===>} prost_convert_3=false;







{=============prosthetic group topology and parameter files===============}

{* prosthetic group topology file *}
{===>} prost_topology_infile_1="fmn.top";
{===>} prost_topology_infile_2="fad.top";
{===>} prost_topology_infile_3="nap.top";

{* prosthetic group parameter file *}
{===>} prost_parameter_infile_1="fmn.par";
{===>} prost_parameter_infile_2="fad.par";
{===>} prost_parameter_infile_3="nap.par";




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