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You will get the error if you do not explicitly specify in the input
files as to where to find the parameter files.
Look for foll. section in all input files (minimize.inp, model_map.inp etc.)
{* parameter files *}
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
{===>} parameter_infile_2="";
{===>} parameter_infile_3="";
If foll. is not specified (which I suspect may be the case), enter
{===>} parameter_infile_2="CNS_TOPPAR:ion.param";
Re-run jobs. That should fix it.
Not sure what's wrong with the map calculation. There is too much going
on with your files and can't tell more without looking at the input
files themselves. Did you manage to read in the HL coefficients?
Raji
U Sam wrote:
Hi Raji,
Thank you.
I could short out Hg into generate.pdb.
Tail of the output is as follows.
ATOM 2849 O ALA 493 38.867 -28.550 1.816 1.00
39.63 BBBB
ATOM 2850 HG HG 757 26.937 -0.022 18.702 1.00
35.00 BBBB
ATOM 2851 HG HG 758 16.790 -15.955 15.878 1.00
35.00 BBBB
ATOM 2852 HG HG 759 36.504 2.463 7.478 1.00
35.00 BBBB
ATOM 2853 HG HG 760 30.646 1.678 7.583 1.00
35.00 BBBB
ATOM 2854 HG HG 761 -4.105 35.153 22.774 1.00
35.00 AAAA
ATOM 2855 HG HG 762 3.201 48.512 34.441 1.00
35.00 AAAA
ATOM 2856 HG HG 763 -2.505 40.737 12.738 1.00
35.00 AAAA
ATOM 2857 HG HG 764 -2.393 23.946 9.440 1.00
35.00 AAAA
When I use this generate.pdb for minimize.inp
I am getting the following error message.
ATOM: SEGId="AAAA", RESId="762 ", NAME="HG ", CHEMical="HG "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="AAAA", RESId="763 ", NAME="HG ", CHEMical="HG "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="AAAA", RESId="764 ", NAME="HG ", CHEMical="HG "
%NBUPDA error encountered: program will be aborted.
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
I 'm also getting same error if I run model_map.inp using the same
generate.pdb
Then taking only protein part of generate.pdb I tried to run
model_map.inp.
But I'm missing the electron density surrounding the chain, I did set
map_cushion=10, map_mode=asymmetric.
And map does not cover complete molecule (if I center a particular
atom, at some point I donot see density surrounding that).
Look for the suggestion.
Thanks
Sam
--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
