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 :
[log in to unmask]"
type="cite">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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