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On 18/04/2012 6:58 AM, sai nitin wrote:
<blockquote
cite="mid:CAGJtc4Mu9178yKG7eqAbEhS5-=KRnx4b0Cv0u4q1MoS+p-J63Q@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
It means exactly what it says. Your coordinate file and topology
must refer to the same system. See last para of manual 5.7.1.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAGJtc4Mu9178yKG7eqAbEhS5-=KRnx4b0Cv0u4q1MoS+p-J63Q@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_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
moz-do-not-send="true" 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>
========================================<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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color="#888888"><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>
Technische Universität Dresden<br>
Tatzberg 47/49<br>
01307 Dresden, Germany<br>
Tel Lab:</span><span>+49 (0)351 463 40060</span><br>
</div>
<br>
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