Jacob,
In CNS/XPLOR all topology files are created equal. You are free to combine all
topology into a single file and read that into CNS. Do you have two copies of
the same ligand or two different ligands? If you have two different ligands,
you can use prodrg or xplo2d/hic-up to generate unique nomenclature for the
topology of each (different chemical identifier characters) and combine the
output to a single file and read that in. If you look how topology files are
read in:
topology
if ( &BLANK%prot_topology_infile = false ) then
@@&prot_topology_infile
end if
if ( &BLANK%nucl_topology_infile = false ) then
@@&nucl_topology_infile
end if
if ( &BLANK%water_topology_infile = false ) then
@@&water_topology_infile
end if
if ( &BLANK%carbo_topology_infile = false ) then
@@&carbo_topology_infile
end if
if ( &BLANK%prost_topology_infile = false ) then
@@&prost_topology_infile
end if
if ( &BLANK%lig_topology_infile = false ) then
@@&lig_topology_infile
end if
if ( &BLANK%ion_topology_infile = false ) then
@@&ion_topology_infile
end if
end
you'll see that no distinction is made anywhere as to what is "ligand" "water"
"ion" etc.
Your later problem during refinement is coming from missing parameter data, not
topology files. CNS knows the topology, but it doesn't have values for the
NONBONDED terms for the atoms in your ligand. Be sure you also read in the
parameter files with the relevant VDW information into the refine.inp script.
That should do it.
Best,
--Paul
--- On Tue, 7/21/09, Jacob Wong <jacob.j.w...@gmail.com> wrote:
> From: Jacob Wong <jacob.j.w...@gmail.com>
> Subject: [ccp4bb] more than one ligands for CNS generate.inp and refine.inp
> files
> To: CCP4BB@JISCMAIL.AC.UK
> Date: Tuesday, July 21, 2009, 3:03 PM
> Dear colleagues, please help
> me with a CNS syntax. In the refine.inp, I could provide as
> many topology (or parameter) files as
> necessary:
> {refine.inp}
> {* topology files *}{===>}
> topology_infile_1="CNS_TOPPAR:protein.top";{===>}
> topology_infile_2="CNS_TOPPAR:dna-rna.top";{===>}
> topology_infile_3="CNS_TOPPAR:water.top";
> {===>}
> topology_infile_4="CNS_TOPPAR:ion.top";{===>}
> topology_infile_5="../data/ligand1.top";{===>}
> topology_infile_6="../data/ligand2.top";
>
> But in the generate.inp file, there is only one
> input option for "ligand" (among others like
> protein,
> water, carbohydrate:{generate.inp}{*
> ligand topology file *}
> {===>}
> ligand_topology_infile="../data/ligand1.top";
> As I'm
> having two ligands in the structure, how do I get around
> with the generate.inp syntax?
>
> Thank
> you in advance, -jacob
>
>
