Thank you all who had kindly reply to me with tips. Basically I was
suggested to combine the two ligand files together, or to "trick" CNS to
take in my 2nd ligand file at like the "prosthetic group" section. The
generate.inp runs without apparent ERR message, but the refinement was
terminated with error like below, apparently with the newer ligand I meant
to put in - the Ethylene Glycol. I was using the Ethylene Glycol files from
HIC Up, links below. I tried putting the EDO files at the authentic ligand
spots but failed as well. Do I need to edit the files after download in
anyway as I'm using CNS v12.? Thank you very much, -jacob
http://xray.bmc.uu.se/hicup/EDO/edo_xplor_top.txt
http://xray.bmc.uu.se/hicup/EDO/edo_xplor_par.txt
MESSage=OFF
ECHO=FALSe {OFF}
Program version= 1.2 File version= 1.2
Maximum of 24848 elements = 0.0000
MAPResolution= 2.8000
GRIDsize= 0.33330
adjusted grid parameter for solvent mask calculation. It is now : 0.321429
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="X ", RESId="1 ", NAME="C1 ", CHEMical="C_1 "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="X ", RESId="1 ", NAME="O1 ", CHEMical="O_2 "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="X ", RESId="1 ", NAME="C2 ", CHEMical="C_3 "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="X ", RESId="1 ", NAME="O2 ", CHEMical="O_4 "
%NBUPDA error encountered: program will be aborted.
(CNS is in mode: SET ABORT=NORMal END)
On 7/21/09, Jacob Wong <[email protected]> wrote:
>
> 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
>
>
>
