<div>Hi Justin,</div><div><br></div><div>I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand topology using swissparam tool using Charmm force field i included ligand.itp file in topol.top of protein. And i used docked complex structure (protein + ligand) from docking analysis and generated boxed.pdb next i created solvated.pdb using (editconf and genbox tools) and also checked SOL molecules updated in topol.top file next i checked solvated.pdb file in pymol my ligand is in correct place in protein the way i wanted but problem came after this while using grompp</div>
<div><br></div><div>I used grompp tool to minimize this solvated.pdb it is showing following error..using em.mdp</div><div><br></div><div>Fatal Error</div>number of coordinates in coordinate file (solvated.pdb, 51540)<br>
does not match topology (topol.top, 52756)<br><br>I know this is commonly known issue for new users of gromacs. I looked up in gmx-archive list couldnt find optimal solution for my problem..<div><br></div><div>Let me know how to solve this ...issue...</div>
<div><br></div><div>Cheers,</div><div>Nitin<br><br><div class="gmail_quote">On Mon, Apr 16, 2012 at 5:03 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
sai nitin wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/complex/01_<u></u>pdb2gmx.html</a> tutorial<br>
<br>
But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology<br>
which is in complex structure.<br>
Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool (<a href="http://swissparam.ch/" target="_blank">http://swissparam.ch/</a>) when i do Editconf and created cubic box ligand is going away from protein.<br>
<br>
Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics.<br>
<br>
Can any body tell me how to do this..?<br>
<br>
</blockquote>
<br></div></div>
Whatever you're doing is changing the coordinates that you originally had. You don't want to do that.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><span><br>Sainitin D</span> <br><span>PhD student<br></span><span>Bioinformatics Group</span><br><span>
</span><span>Biotechnology Center</span><br><span>
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