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[X-plor] Including Two ligands in CNS generate.inp file

Shankar Prasad Kanaujia spk at rishi.serc.iisc.ernet.in
Sun May 21 04:31:22 EST 2006


Dear users,
I am refining my model using CNS (version 1.1). I have density for two 
different ligands. So, I made two files lig1.pdb & lig2.pdb and also generated 
topology and parameter files using HIC-UP server. Now, I included these 
two (lig1.pdb & lig2.pdb) in my generate.inp file in the ligand section 
and .top and .par files also in the ligand parameter section. But it is 
not working. 

The error it is giving that residue TRS (lig1) and MPD (lig2) 
is not found  in the molecular structure. 
The necessay lines of my generate.inp files are like this
/* 
{============================ protein files ================================}

{* Multiple coordinate files of the same type can be defined by duplicating
   all of the entries below and incrementing the file number *}
{* protein coordinate file *}
{===>} prot_coordinate_infile_1="protein.pdb";
{* rename segid *}
{+ choice: true false +}
{===>} prot_rename_1=false;
{* new segid *}
{===>} prot_segid_1="";
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} prot_convert_1=false;
{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===>} prot_separate_1=true;
{============================= water files =================================}
{* Multiple coordinate files of the same type can be defined by duplicating
   all of the entries below and incrementing the file number *}
{* water coordinate file *}
{===>} water_coordinate_infile_1="water.pdb";
{* rename segid *}
{+ choice: true false +}
{===>} water_rename_1=false;
{* new segid *}
{===>} water_segid_1="";
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} water_convert_1=false;
{============================ ligand files =================================}
{* Multiple coordinate files of the same type can be defined by duplicating
   all of the entries below and incrementing the file number *}
{* ligand coordinate file *}
{===>} lig_coordinate_infile_1="lig1.pdb";
{===>} lig_coordinate_infile_2="lig2.pdb";
{* rename segid *}
{+ choice: true false +}
{===>} lig_rename_1=false;
{* new segid *}
{===>} lig_segid_1="";
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} lig_convert_1=false;
{============================== ions files =================================}
{* Multiple coordinate files of the same type can be defined by duplicating
   all of the entries below and incrementing the file number *}
{* ion coordinate file *}
{===>} ion_coordinate_infile_1="metal.pdb";
{* rename segid *}
{+ choice: true false +}
{===>} ion_rename_1=false;
{* new segid *}
{===>} ion_segid_1="";
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} ion_convert_1=false;
{============================= output files ================================}
{* output structure file *}
{===>} structure_outfile="gen.mtf";
{* output coordinate file *}
{===>} coordinate_outfile="gen.pdb";
{* format output coordinates for use in o *}
{* if false then the default CNS output coordinate format will be used *}
{+ choice: true false +}
{===>} pdb_o_format=true;
{================== protein topology and parameter files ===================}

{* protein topology file *}
{===>} prot_topology_infile="CNS_TOPPAR:protein.top";
{* protein linkage file *}
{===>} prot_link_infile="CNS_TOPPAR:protein.link";
{* protein parameter file *}
{===>} prot_parameter_infile="CNS_TOPPAR:protein_rep.param";

{================ nucleic acid topology and parameter files =================}

{* nucleic acid topology file *}
{===>} nucl_topology_infile="CNS_TOPPAR:dna-rna.top";
{* nucleic acid linkage file *}
{* use CNS_TOPPAR:dna-rna-pho.link for 5'-phosphate *}
{===>} nucl_link_infile="CNS_TOPPAR:dna-rna.link";
{* nucleic acid parameter file *}
{===>} nucl_parameter_infile="CNS_TOPPAR:dna-rna_rep.param";

{=================== water topology and parameter files ====================}

{* water topology file *}
{===>} water_topology_infile="CNS_TOPPAR:water.top";
{* water parameter file *}
{===>} water_parameter_infile="CNS_TOPPAR:water_rep.param";

{================= carbohydrate topology and parameter files ===============}

{* carbohydrate topology file *}
{===>} carbo_topology_infile="CNS_TOPPAR:carbohydrate.top";
{* carbohydrate parameter file *}
{===>} carbo_parameter_infile="CNS_TOPPAR:carbohydrate.param";

{=================== ligand topology and parameter files ===================}

{* ligand topology file *}
{===>} lig_topology_infile_1="lig1.top";
{===>} lig_topology_infile_2="lig2.top";
{* ligand parameter file *}
{===>} lig_parameter_infile_1="lig1.par";
{===>} lig_parameter_infile_2="lig2.par";

{===================== ion topology and parameter files ====================}

{* ion topology file *}
{===>} ion_topology_infile="CNS_TOPPAR:ion.top";
{* ion parameter file *}
{===>} ion_parameter_infile="CNS_TOPPAR:ion.param";

{===========================================================================}
{         things below this line do not need to be changed unless           }
{         you need to apply patches - at the appropriate places marked      }
{===========================================================================}

 ) {- end block parameter definition -}

*/

It will be very helpful if somebody give the suggestion how to solve this 
problem. 
Thanking you all.

Your Sincerely,
Shankar Prasad Kanaujia.



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