Hi, I've recently compiled an OpenMP version of CNS 1.21 using ifort (version 10.1.0.15). It works nicely with minimize.inp and bindividual.inp, and total time...
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 9:24 pm
1722
Dear Prof. Axel Brunger, Thank you very much for your suggestion! ... enabled the program to run and terminate normally. Best regards, kami...
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 10:42 pm
1723
Hi all I am getting this error while installing CNS in kubuntu 8.02... Installation directory: /usr/local/bin/cns_solve_1.21/intel-i686-linux copying files in...
Hi Navdeep, I had the same problems on an openSUSE machine. Try the Intel compiler ifort. http://www.intel.com/cd/software/products/asmo-na/eng/282048.htm Also...
Hi, I am a new member to this group and have a calculation problem with CNS 1.2. When proton chemical shifts are added as a constraint, the overall energy in...
Hi Thanks for to Dr. Chavas, Dr. Mark and Dr Shaanan for your suggestions. I want to run make_cv.inp to start refinement in CNS.I have converted my mtz data...
Hi , running minimize.inp in cns 1.2 I get the output .pdb file I need but at the end of the .log file I get this error : %FREHP error encountered: corrupt...
Please try the most recent version (1.21). Axel Brunger ... Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular...
Axel Brunger
brunger@...
Aug 12, 2008 2:41 pm
1729
Hello Everyone, Can anyone suggest me how to calculate average structure and rmsd of an ensemble of structures (say 10) obtained from simulated annealing? I...
Hello, while trying to run a 'standard' refine.inp script, I got the following message: MAPResolution= 2.1500 GRIDsize= 0.33330 grid parameter for solvent...
Filip Van Petegem
filip.vanpetegem@...
Aug 18, 2008 5:36 am
1731
Are you using an external solvent mask? Your external mask may not be properly defined. Try to use an internal mask. Axel Brunger ... Axel T. Brunger ...
Axel Brunger
brunger@...
Aug 18, 2008 2:48 pm
1732
Your test case ran fine on my mac. So I suspect it is a machine/compilation problem. How did you compile CNS on your linux computer? Which compiler did you...
Axel Brunger
brunger@...
Aug 18, 2008 11:11 pm
1733
Hello, I'm not using an external mask, but the problem goes away when I switch off bulk solvent scaling and truncate at 8A. Because my data at low resolution ...
Filip Van Petegem
filip.vanpetegem@...
Aug 19, 2008 5:22 am
1734
Hi I want to convert "car and mdf" or "msi" files generated using materials studio to "pdb and psf" files. Please help me in doing so. Thanks...
Hi Rupi, I have never converted these files myself but have a look into the openbabel project. It might do what you need. http://openbabel.org Cheers, ...
We have 4 million small molecules in pdb format, with many more to come. Check it out. http://molecules.gnu-darwin.org/ Be sure and scroll down to the News...
proclus@...
Aug 20, 2008 4:51 am
1737
I am starting to get questions about how the Molecules site was constructed. http://molecules.gnu-darwin.org/ I think that it is a good example of what is...
Molecules@... site in...
proclus@...
Aug 21, 2008 6:16 pm
1738
Hi all I am trying to generate psf file for carbon nanotubes but the atom types are not defined on the force field files. How can I generate these files. ...
Hi I am trying to refine the experimental model (few helices) using cns1.1 and cns rigid body and model map throw away the model out of the density and map...
I am a CNS 1.21 user. Recently I want to check if there is a small molecule in my protein and I did the sa_omit_map.inp in CNS.But when I opened the...
Dear Albumns -- ... This is a question for the Coot mailing list I guess. Anyway, in this case I think I can give a hint... it should depend on your resolution...
Leo Chavas
cnshnaalas@...
Aug 25, 2008 11:19 am
1742
Hi all, When I run generate.inp script in CNS 1.21, I get the message "Segmentation fault". The last lines in the output file are CNSsolve> do...
This sounds to me like a compiler problem on your linux computer. Please use the latest Intel ifort, Portland Group pgf95, or Gfortran compilers on linux. I...
Axel Brunger
brunger@...
Sep 9, 2008 9:12 pm
1744
One more thing: please make sure you set limit stacksize unlimited on your machine. The default stacksize is often too small, causing unpredictable...
Axel Brunger
brunger@...
Sep 9, 2008 9:13 pm
1745
Hi all I have seen several messages without answer concerning how to deal with atoms on special position. Can somebody tell clearly what is going on when atoms...
Dear all: Rcently I want to judge if there is a ligand in my structure, and make 2fo-fc and omit map by CNS1.21. When I opened then in Coot, it found that:...
Deal all CNS users, I want to refine a solution NMR structure with CNS 1.2. The final CNS energy of this struture is shown below: REMARK overall = 532.641 ...
Dear Albumns -- ... How did you solve the structure of the complex with the ligand? I would say, personally, that the omit map is trustful, as it is its ...
Leo Chavas
cnshnaalas@...
Sep 23, 2008 6:20 am
1749
Hi, I am using cns1.1 to refine a protein nmr structure, employing aria as a front. I routinely get tons of violations in dihedral angles: Number of violations...
