Thanks. <br><br>I used the PDB file with H . It works though it's still a mystery for me why PDB file without H couldn't work.<br> <br><br><br><div class="gmail_quote">On Tue, Jan 20, 2009 at 1:53 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;"><br>
<br>
Liu Shiyong wrote:<br>
<br>
<snip><br>
<br>
The problem lies here:<div class="Ih2E3d"><br>
<br>
Including chain 1 in system: 1296 atoms 125 residues<br>
Including chain 2 in system: 1274 atoms 123 residues<br>
Including chain 3 in system: 2085 atoms 201 residues<br>
<br></div>
This suggests that chain 2 (Protein B) should contain numbers up to about 2500.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
ATOM 1996 O ASN B 248 49.634 9.874 85.195 1.00 0.00<br>
ATOM 1997 OXT ASN B 248 50.217 10.536 83.158 1.00 0.00<br>
TER<br>
ATOM 1998 N GLY C 249 70.273 30.186 73.098 1.00 0.00<br>
ATOM 1999 CA GLY C 249 68.973 30.327 72.421 1.00 0.00<br>
<br>
</blockquote>
<br></div>
This is the original .pdb file, then? The hydrogens will be missing from the appropriate groups in the pdb2gmx-processed output structures. You can check the numbering (and pertinent charge groups) in the topology for each chain, to be sure.<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
make_ndx -f ${df}.pdb -o ${file}.ndx ><br>
${file}.output.make_ndx<br>
<< _EOF_<br>
del 0-9<br>
chain A and B<br>
chain C<br>
q<br>
_EOF_<br>
</blockquote>
<br></div>
This should work, with the right input :)<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="Wj3C7c"><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>
</div></div></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>