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.<div>
<br></div><div>Some of the common formatting problems that throw this type of error include:</div><div>1. Input coarse grain template:</div><div> 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.</div>
<div> b. Make sure there is one *and only one* END or TER at the end of the file.</div><div>2. Input full atomic reference structure:</div><div> a. Make sure that there are *only* ATOM lines in the file. Remove all comments or non-RNA lines.</div>
<div> b. Make sure that there are no repeated atom and residue numbers.</div><div> 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.</div>
<div>3. -FD.txt fragment definition file.</div><div> a. Make sure that there are no blank lines.</div><div> 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.</div>
<div><br></div><div>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.</div><div><br></div><div>
-Magda</div><div><br></div><div>P.S. These instructions have been added to the NAST wiki at <a href="http://simtk.org/homer/nast">simtk.org/homer/nast</a>.</div><div><div><br><div class="gmail_quote">On Tue, Mar 16, 2010 at 5:56 AM, subarna thakur <span dir="ltr"><<a href="mailto:bubli_thakur@rediffmail.com">bubli_thakur@rediffmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br>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-<br>
self.FirstRes=self.resList[0].<br>Can you please help me to solve the problem<br>regards<br><font color="#888888">Subarna<br></font><br>_______________________________________________<br>
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