Dear Justin,<br><br>I built .rtp entries for two ligands using (<a href="http://davapc1.bioch.dundee.ac.uk/prodrg/" target="_blank">http://davapc1.bioch.dundee.ac.uk/prodrg/</a>). I added to the topol.top the following parts:<br>
#include "TRS.itp"<br>#include "EDO.itp"<br>TRS 1<br>EDO 6<br>Furthermore I added the number of atoms (20) in the second line of the .gro file. may <span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">the problem</span> <span title="Alternatif çevirileri görmek için tıklayın">related to</span> <span title="Alternatif çevirileri görmek için tıklayın">pdb</span> <span title="Alternatif çevirileri görmek için tıklayın">file (3NM4.pdb)? Because </span></span> -OH groups seems as -O. isn't it?
<span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">maybe</span> <span title="Alternatif çevirileri görmek için tıklayın">I'm wrong. </span></span><span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">What</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">would you recommend?<br>
<br></span></span><div class="gmail_quote">
2011/4/14 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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><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>
pdb2gmx -f xxx.pdb<br>
water:spc<br>
forcefield:43a1<br>
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro<br>
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro<br>
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br>
*Fatal error:*<br>
number of coordinates in coordinate file (solvated.gro, 106523) does not match topology (topol.top, 106553)<br>
I look at gmx-user search. But I dont be able to solved the problem. Then I look at conf.gro and box.gro. I recognised the there is not the TRS ligand in the box.gro file. What reason?<br>
<br>
</blockquote>
<br></div>
Based on your workflow, it looks as is you never added it in. If conf.gro came from pdb2gmx, did you build .rtp entries for your ligands, or just #include .itp files after the fact? If the latter, then you have to modify the coordinate file (conf.gro) to include these molecules. If you did this but did not correctly increment the number of atoms in the second line of the .gro file, likely anything with a higher atom number got truncated. If the conf.gro file you show below is indeed what you used, though, I see no reason why this should have happened except that perhaps you left out a step you thought you had done previously.<br>
<br>
The difference in the coordinate file vs. topology is 30 atoms, which is more than both of your ligands (20 atoms), so your problem likely lies elsewhere.<br>
<br>
-Justin<div><div></div><div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
<br>
_*conf.gro:*_<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>
1EDO OAB 1 0.625 -3.071 -0.171<br>
1EDO HAA 2 0.698 -3.048 -0.107<br>
1EDO CAA 3 0.596 -3.211 -0.163<br>
1EDO CAC 4 0.486 -3.247 -0.261<br>
1EDO OAD 5 0.365 -3.179 -0.224<br>
1EDO HAB 6 0.292 -3.203 -0.288<br>
1TRS O1 1 1.825 -3.900 0.047<br>
1TRS HAA 2 1.853 -3.860 -0.040<br>
1TRS C1 3 1.712 -3.977 0.028<br>
1TRS C 4 1.659 -4.044 0.150<br>
1TRS C3 5 1.576 -3.946 0.226<br>
1TRS O3 6 1.634 -3.824 0.256<br>
1TRS HAC 7 1.569 -3.768 0.307<br>
1TRS N 8 1.582 -4.159 0.113<br>
1TRS HAE 9 1.547 -4.204 0.195<br>
1TRS HAF 10 1.505 -4.131 0.056<br>
1TRS HAD 11 1.639 -4.223 0.062<br>
1TRS C2 12 1.776 -4.085 0.233<br>
1TRS O2 13 1.887 -4.122 0.160<br>
1TRS HAB 14 1.961 -4.148 0.222<br>
8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000 0.00000 0.00000<br>
<br>
<br>
<br>
<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br></div></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 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>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>