[Nast-news] error in c2a

[Magdalena Jonikas]

C2A is very picky about the format of the input files and will throw "list
index out of range" errors when there is something wrong with an input
file. Unfortunately the error messages are not very helpful to the user at
the moment, and we are planning on fixing that in a future version.

Some of the common formatting problems that throw this type of error
include:
1. Input coarse grain template:
  a. ATOM line formatting - make sure your formatting matches that of the
c2a example input coarse-grain template. In particular, check the positions
of the atom type 'C3*' and atom/residue numbers.
  b. Make sure there is one *and only one* END or TER at the end of the
file.
2. Input full atomic reference structure:
  a. Make sure that there are *only* ATOM lines in the file. Remove all
comments or non-RNA lines.
  b. Make sure that there are no repeated atom and residue numbers.
  c. Make sure that separate chains are separated by at least one atom and
residue number so that c2a knows the residues are not connected.
3. -FD.txt fragment definition file.
  a. Make sure that there are no blank lines.
  b. Make sure that there are no 1-base-pair long helices. You can fix this
by either lengthening the definition of the helix fragment beyond the actual
length of the helix, or by removing the helix and letting those residues be
parts of junction fragments.

I hope this helps, if none of these suggestions fix your problem, send me
your input files (coarse grain template, full atomic reference and -FD.txt)
so I can help troubleshoot.

-Magda

P.S. These instructions have been added to the NAST wiki at
simtk.org/homer/nast.

On Tue, Mar 16, 2010 at 5:56 AM, subarna thakur <bubli_thakur at rediffmail.com
> wrote:

> Hi,
> I have generated a pdb file containing a coarse grain model of a tRNA.But
> when I am running the first step of C2a for finding fragment match with pdb
> file as reference,I am getting an error.I have taken a crystal structure of
> tRNA(1Wz2) as reference. The name of the pdb file has been mentioned in
> searchstructurefile section of the ex1.py script.As I am running the ex1.py
> script,I am getting an error which states-IndexError: list lindex out of
> range. The error seems to be present in line 324 of ca.py script which bear
> the following line-
> self.FirstRes=self.resList[0].
> Can you please help me to solve the problem
> regards
> Subarna
>
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