Hello Edward,
I am not really certain for my explanation, but your error message about
the namelist could be provoked by a problem in your input files. In fact
you have to oriented each strand and define limits of the two strands.
If you do a mistake with the orientation you can have this type of
message. You can try different combination with this part of your
command line :
2 1 -1 0 0
1: 12
24:13
Maybe the key could be in this part of your command line atless for the
input error message.
To my mind you have to edit your input file because its format is not
adaptated for this programm. The format wich is too recent or with to
much informations are not well suported.
I hope i help you.
Sincerly . Nicolas
Le 03/02/11 21:05, Eddie Pryor a écrit :
Hi, All,
I am trying to analyze DNA from a recent structure with the program
Curves+ (R. Lavery et al, Nuc. Acids. Res (2009) 37:17 5917;
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html). I have downloaded
the files, and untarred them to a directory "curves" on my machine.
Running the Make command on these files yielded no errors, and I have
the executable file Cur+ in this directory. I am trying to run this
program, first using the example data that is provided (the
Drew-Dickerson Dodecamer), but am having some difficulties. The
resource for Curves gives the following command to run the program:
/Users/RL/Code/Cur+ <<!
&inp file=str/1bna, lis=r+bdna,
lib=/Users/RL/Code/standard,
&end
2 1 -1 0 0
1: 12
24:13
!
On my machine, the directory structure is slightly different:
- the executable Cur+ is in a folder named "curves"
- the files standard_b.lib and standard_s.lib are also in this folder
- the pdb file 1bna.pdb is in the subfolder "data"
I have tried to run the program by doing the following:
[xxxxx@zeus ~/curves]$ Cur+ <<!
? &inp file=data/1bna, lis=r+bdna,
? lib=standard, &end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
The question mark prompts appear upon hitting enter after each line.
The only error message I get when I try to run this is:
---- Error in namelist input for ----
I have even tried the following (entering all if the input files on
the same line):
[xxxxx@zeus ~/curves]$ Cur+ <<! &inp file=data/1bna, lis=r+bdna,
lib=standard, &end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
Which gives the following errors:
inp: Command not found
end: Not in while/foreach
At line 28 of file nml.f
Fortran runtime error: End of file
I am hoping that some of you have had success with running this
program and can offer any advice. I would really appreciate it!
Thanks!
Edward Pryor
Ph.D. Candidate
Tom Hollis Lab
Department of Biochemistry
Center for Structural Biology
Wake Forest University School of Medicine
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