Dear Tsjerk,<br><br>I will ask you one thing but <span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">please do</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">not get angry (</span></span><span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">I know</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">you are not a</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">private</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">tutor</span></span> but I need your helps).<br>
<span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps"><br>How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?)<br>
<br>Thanks<br></span></span><br><div class="gmail_quote">2011/3/31 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 31/03/2011 5:18 PM, ahmet yıldırım wrote:
<blockquote type="cite">Dear users,<br>
<br>
Before energy minimization step , I performed the preprosessing
step using grompp .<br>
However, there are two note that :<br>
<br>
<b><u>NOTE 1 [file topol.top, line 52]:</u></b><br>
System has non-zero total charge: -1.500000e+01<br>
</blockquote>
<br></div>
This is an integer. See
<a href="http://en.wikipedia.org/wiki/Scientific_notation#E_notation" target="_blank">http://en.wikipedia.org/wiki/Scientific_notation#E_notation</a> and
<a href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic" target="_blank">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a> <br><div class="im">
<br>
<blockquote type="cite"><u><b>NOTE 2 [file topol.top]:</b></u><br>
The largest charge group contains 11 atoms.<br>
Since atoms only see each other when the centers of geometry of
the charge<br>
groups they belong to are within the cut-off distance, too large
charge<br>
groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a
few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,
CO, etc.<br>
</blockquote>
<br></div>
See Tsjerk's email.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite"><b><br>
PS: </b>TRS and EDO are not aminoacid<b><br>
<br>
<u>TRS.itp:</u></b><br>
..<br>
[ moleculetype ]<br>
; Name nrexcl<br>
TRS 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 1 TRS O1 1 -0.119 15.9994 <br>
2 H 1 TRS H13 1 0.032 1.0080 <br>
3 CH2 1 TRS C1 1 0.087 14.0270 <br>
4 CCl4 1 TRS C 2 0.055 12.0110 <br>
5 CH2 1 TRS C3 2 0.049 14.0270 <br>
6 OA 1 TRS O3 2 -0.205 15.9994 <br>
7 H 1 TRS H33 2 0.019 1.0080 <br>
8 NL 1 TRS N 2 0.206 14.0067 <br>
9 H 1 TRS H2 2 0.004 1.0080 <br>
10 H 1 TRS H3 2 0.004 1.0080 <br>
11 H 1 TRS H1 2 0.004 1.0080 <br>
12 CH2 1 TRS C2 2 0.050 14.0270 <br>
13 OA 1 TRS O2 2 -0.205 15.9994 <br>
14 H 1 TRS H23 2 0.019 1.0080 <br>
...<br>
<br>
<u><b>EDO.itp</b></u><br>
...<br>
[ moleculetype ]<br>
; Name nrexcl<br>
EDO 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 1 EDO OAB 1 -0.111 15.9994 <br>
2 H 1 EDO HAE 1 0.031 1.0080 <br>
3 CH2 1 EDO CAA 1 0.080 14.0270 <br>
4 CH2 1 EDO CAC 1 0.080 14.0270 <br>
5 OA 1 EDO OAD 1 -0.111 15.9994 <br>
6 H 1 EDO HAF 1 0.031 1.0080 <br>
...<br>
<u><b><br>
topol.top:</b></u><br>
..<br>
; Include water topology<br>
#include "gromos43a1.ff/spc.itp"<br>
#include "TRS.itp"<br>
#include "EDO.itp"<br>
..<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
SOL 185<br>
SOL 143<br>
TRS 1<br>
EDO 1<br>
SOL 44125<br>
<b><u><br>
Conf.gro:</u></b><br>
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br>
5354<br>
2GLN N 1 1.458 -1.158 0.739<br>
2GLN H1 2 1.520 -1.083 0.763<br>
.......<br>
485HOH HW1 5333 0.221 -3.864 -2.291<br>
485HOH HW2 5334 0.303 -3.946 -2.407<br>
1TRS O1 1 -3.812 -0.471 -2.002<br>
1TRS H13 2 -3.865 -0.443 -1.922<br>
1TRS C1 3 -3.672 -0.469 -1.971<br>
1TRS C 4 -3.635 -0.571 -1.863<br>
1TRS C3 5 -3.711 -0.547 -1.731<br>
1TRS O3 6 -3.694 -0.414 -1.679<br>
1TRS H33 7 -3.746 -0.404 -1.594<br>
1TRS N 8 -3.673 -0.705 -1.911<br>
1TRS H2 9 -3.625 -0.725 -1.996<br>
1TRS H3 10 -3.771 -0.707 -1.927<br>
1TRS H1 11 -3.649 -0.774 -1.842<br>
1TRS C2 12 -3.483 -0.573 -1.840<br>
1TRS O2 13 -3.428 -0.445 -1.806<br>
1TRS H23 14 -3.470 -0.412 -1.722<br>
1EDO OAB 1 0.307 -2.792 0.149<br>
1EDO HAE 2 0.390 -2.826 0.104<br>
1EDO CAA 3 0.239 -2.901 0.212<br>
1EDO CAC 4 0.111 -2.851 0.281<br>
1EDO OAD 5 0.144 -2.763 0.388<br>
1EDO HAF 6 0.060 -2.731 0.432<br>
8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550
0.00000 0.00000 0.00000<br clear="all">
<br>
How can I fixed these notes(note 1 and note 2)?<br>
<br>
Thanks in advance<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
</div></div></div>
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