Thanks. <br><br> Summary:<br><br> 1) *.gro from pdb2gmx has no chain id information<br> 2) pdb2gmx has an option to output pdb file <br> 3) If you want to make groups based on chain id :<br><br> pdb2gmx -ignh -ff ${forcefield} -f input.pdb -o a.pdb <br>
make_ndx -f a.pdb -o a.ndx > a.output.make_ndx <br> <br> 4) mdrun has an option to output the minimized structure.<br> <br> Thanks to all.<br><br><br><br><br><div class="gmail_quote">On Thu, Jan 29, 2009 at 12:26 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>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
*.gro has no chain id information.<br>
I can not make energy group(based on chain id) from *.gro file generated by pdb2gmx<br>
</blockquote>
<br></div>
See the mail I just sent.<div><div></div><div class="Wj3C7c"><br>
<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>
<br>
3. Don't strip H, just to add them back again :)<br>
<br>
<br>
I have the structure minimized.pdb after EM.<br>
<br>
minimized.pdb is output from mdrun with -c option.<br>
<br>
I tried to feed this structure into pdb2gmx.<br>
I got an error.<br>
<br>
Processing chain 1 'A' (5360 atoms, 535 residues)<br>
There are 803 donors and 760 acceptors<br>
There are 1025 hydrogen bonds<br>
Will use HISB for residue 212<br>
Will use HISB for residue 223<br>
Will use HISB for residue 277<br>
Will use HISB for residue 280<br>
Will use HISB for residue 374<br>
Will use HISB for residue 380<br>
Will use HISB for residue 386<br>
Will use HISB for residue 398<br>
Will use HISB for residue 425<br>
Will use HISB for residue 440<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3.3<br>
Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421<br>
<br>
Fatal error:<br>
Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms<br>
while sorting atoms. Maybe different protonation state.<br>
Remove this hydrogen or choose a different protonation state.<br>
Option -ignh will ignore all hydrogens in the input.<br>
-------------------------------------------------------<br>
<br>
</blockquote>
<br></div></div>
Without -ignh, pdb2gmx expects all atoms to present and appropriately named. This is one of the more useful error messages, since it tells you exactly how to fix the problem.<div class="Ih2E3d"><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></div><div><div></div><div class="Wj3C7c">
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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</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>