Hi,<br><br>Did you get my script ? <br>I dump a frame from .trr file.<br>I did not define xtc-grps<br> <br><br><div class="gmail_quote">On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
<br>
Liu Shiyong wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command.<br>
<br>
</blockquote>
<br></div>
<snip><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.3<br>
Source code file: ../../../../src/kernel/readir.c, line: 838<br>
<br>
*Fatal error:<br></div>
Invalid atom number 6415 in indexfile*<br>
-------------------------------------------------------<br>
<br>
</blockquote>
<br>
Instead of screen dumps, it would be a lot more useful to see your .mdp file, as well as the command line (not output from) both grompp and trjconv. Did you dump the frame from an .xtc file? What did you specify in xtc-grps?<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:         (785) 864-1962<br>