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On 17/04/2011 7:05 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:BANLkTimgwhHsd9qGw7w_Jhy=J1bhj6R+Aw@mail.gmail.com"
type="cite">Dear Justin,<br>
<br>
I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files
for each EDO molecule using prodrg web server. I am adding
coordinates of each EDO molecule into a file called conf.gro. The
conf.gro file is obtained from without_EDO_TRS. pdb ( there is not
ligands). is this procedure correct?<br>
<br>
<span id="result_box" class="short_text" lang="en"><span
title="Alternatif çevirileri görmek için tıklayın" class="hps">I
do not know</span> <span title="Alternatif çevirileri görmek
için tıklayın" class="hps">what to do</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">about</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">EDO.itp because </span></span><span
id="result_box" class="" lang="en"><span title="Alternatif
çevirileri görmek için tıklayın" class="hps">.itp</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">files</span>
obtained <span title="Alternatif çevirileri görmek için
tıklayın" class="hps">from the prodrg web server</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">are
the same</span></span>. <span id="result_box"
class="short_text" lang="en"><span title="Alternatif çevirileri
görmek için tıklayın" class="hps">How can I</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">create</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">one</span> .itp <span title="Alternatif
çevirileri görmek için tıklayın" class="hps">file</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">for</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">all the</span> <span title="Alternatif çevirileri
görmek için tıklayın" class="hps">EDO molecules</span><span
class="" title="Alternatif çevirileri görmek için tıklayın">?</span></span><br>
</blockquote>
<br>
A molecule .itp file can contain the [moleculetype] for that
molecule. It has a name given to it inside the [moleculetype]. This
molecule is replicated by grompp according to the number assigned
next to the reference to the name in the [molecules] section.<br>
<br>
Your .top file could look something like this.<br>
<br>
#include "whatever/forcefield.itp"<br>
#include "whateverprotein.itp"<br>
#include "trs.itp"<br>
#include "edo.itp"<br>
#include "somewater.itp"<br>
<br>
[molecules]<br>
Protein 1<br>
EDO 6<br>
TRS 1<br>
SOL 23445<br>
<br>
Read the examples in chapter 5, do some tutorials without trying to
modify them, and you will better understand the forms that .top
files can take.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimgwhHsd9qGw7w_Jhy=J1bhj6R+Aw@mail.gmail.com"
type="cite">
<br>
Thanks<br>
<br>
<br>
<div class="gmail_quote">16 Nisan 2011 02:08 tarihinde Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Dear users,<br>
<br>
Is there anyone has a tutorial of the ligand have more
than one molecules?<br>
</blockquote>
<br>
</div>
Perhaps you can describe in more detail what it is you hope to
accomplish. The procedure for dealing with multiple ligands
is, in principle, no different from a single ligand. There
are not tutorials available for every variation of a
procedure.<br>
<br>
-Justin
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
For example:<br>
*_topol.top:_*<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
*ligandname * 3<br>
<br>
Thanks in advance<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br>
</div>
-- <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>
========================================<br>
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</font></blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
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