I have installed Haddock 2.1 on my system along with following recommended softwares.
During initialization, air.tbl, new.html and run.cns files were made correctly. But when I typed haddock2.1 in the directory containing run.cns file, following error came.
waiting for /home/combio/sufian/01-yoon2013/run1/begin/3RYO-A_clean_set.pdb...
waiting for /home/combio/sufian/01-yoon2013/run1/begin/3RYO-A_clean_set.psf...
waiting for /home/combio/sufian/01-yoon2013/run1/begin/2VSW_clean_set.pdb...
waiting for /home/combio/sufian/01-yoon2013/run1/begin/2VSW_clean_set.psf...
Error in the topology generation: prot_psf_A could not be created
=> HADDOCK stopped
Within /run1/begin/ directory, 2 generate_*.out files were made containing following error;
%SETFPEPS increase value of MXFPEPS2 and recompile
%SETFPEPS error encountered: Could not determine machine epsilon
I searched internet and found following two links useful;
https://groups.yahoo.com/neo/groups/cnsbb/conversations/topics/2093
https://groups.yahoo.com/neo/groups/cnsbb/conversations/topics/2198
I modified /usr/local/cns_solve_1.3/source/machvar.inc file
old = PARAMETER (MXFPEPS2=1024)
new = PARAMETER (MXFPEPS2=4096)
and recompiled CNS using the command;
make install
But still error persists. Everytime I removed run1/ directory so that new run1 be made. So how to overcome this issue ?
I think I need to write a number other than 4096 specific to my system. Kindly guide me. My system specifications are;
Processor: x86_64
Operating-system: GNU/Linux
Kernel: Linux 3.4.63-2.44-desktop
You may have to run "make clean" before running the "make install" command, otherwise the changes will not be applied. I hope this helps.
Thank you Raquel Dias for a clever solution, but there was some error while performing 'make clean'.
### ISSUE RESOLVED ###
Modify the /cns_solve_1.3/source/machvar.f like this (line numbers on the left).
65 ONEP = DPTRUNC(ONE) + DPTRUNC(FPEPS)
66 ONEM = DPTRUNC(ONE) - DPTRUNC(FPEPS)
******* WRITE (6,'(I6,E10.3,E10.3)') I, ONEP, ONEM
67 IF (ONE .EQ. ONEP .OR. ONE .EQ. ONEM) THEN
68 I = I - 1
Recompile CNS and run HADDOCK.
Courtesy:
https://groups.yahoo.com/neo/groups/cnsbb/conversations/topics/2124 (specially Dr. Sunil Kr. Tewary)
Hi Muhammad,
I've not had the pleasure of compiling CNS and HADDOCK for a while now, so unfortunately I'm too far behind the times to offer you help in that respect, however have you considered using the haddock web server - it should at least free you from any installation woes, and will probably complete your job faster.
Good luck
Andy
Hello Muhammed,
I am getting the same error, did you figure out a good way to deal with it. Is it really an installation problem.
The server is not good solution if you have lots of jobs.
Regards
Marawan
Dear Mr.Marawan,
I have already mentioned the solution in my post dated Feb 18, 2015. You need to modify the file machvar.f by adding a line starting with WRITE.
Hello everyone,
I also got these errors and was able to resolve them.
Just take care of installation steps of CNS:
-> After registration, download xyz.tar.gz file "xyz = cns_solve downloaded version"
-> Enter the command in terminal: `gunzip xyz.tar.gz`
-> Then enter: `tar xvf xyz.tar`
-> This will create a new cns_solve directory. Now enter into this directory and copy the path.
-> Now open the file cns_solve_env and paste the copied path in place of 'location of CNSsolve directory'
-> Then open the terminal in this directory, and enter the command:`tcsh`
-> Then you entered into C-shell, now enter the command: `source cns_solve_env`
->Then enter: `cns`
-> Your software will definitely run without any error.
- Badges
- Science topic
- Similar topics
- Philosophy
- Esthetics
- Interpretation