Dear Justin,<br><br>Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake?<br><br><u><b>conf.gro:</b></u><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><br> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000 0.00000 0.00000<br><br><div class="gmail_quote">14 Nisan 2011 20:15 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdý:<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 yýldýrým 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 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>
</blockquote>
<br></div>
Well, either pdb2gmx built the molecules into your topology or you're #including them in this manner, you should not do both.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
TRS 1<br>
EDO 6<br>
</blockquote>
<br>
So this is part of your [molecules] directive? If you've got six copies of EDO, that's likely where the disconnect comes from - you only had one in your previous coordinate file snippet.<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;">
Furthermore I added the number of atoms (20) in the second line of the <br>
</blockquote>
<br></div>
If you have 6 EDO, the necessary addition is more than just 20.<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;">
.gro file. may the problem related to pdb file (3NM4.pdb)? Because -OH groups seems as -O. isn't it? maybe I'm wrong. What would you recommend?<br>
<br>
</blockquote>
<br></div>
Generally H atoms are not present in crystal structures. If your ligands require certain H atoms, then you must do one of two things:<br>
<br>
1. Add all the necessary hydrogen atoms to the protein and ligands and run pdb2gmx.<br>
<br>
2. Have no H atoms present in the initial coordinate file and build suitable .hdb entries for your ligands so they will be constructed from existing atoms.<br>
<br>
It seems like you're applying several different methods at once. There are protein-ligand tutorials that you may find useful for keeping all of this straight (I recommend my own):<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems" target="_blank">http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2011/4/14 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div></div><div class="h5"><br>
<br>
<br>
<br>
ahmet yýldýrým wrote:<br>
<br>
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)<br>
does not match topology (topol.top, 106553)<br>
I look at gmx-user search. But I dont be able to solved the<br>
problem. Then I look at conf.gro and box.gro. I recognised the<br>
there is not the TRS ligand in the box.gro file. What reason?<br>
<br>
<br>
Based on your workflow, it looks as is you never added it in. If<br>
conf.gro came from pdb2gmx, did you build .rtp entries for your<br>
ligands, or just #include .itp files after the fact? If the latter,<br>
then you have to modify the coordinate file (conf.gro) to include<br>
these molecules. If you did this but did not correctly increment<br>
the number of atoms in the second line of the .gro file, likely<br>
anything with a higher atom number got truncated. If the conf.gro<br>
file you show below is indeed what you used, though, I see no reason<br>
why this should have happened except that perhaps you left out a<br>
step you thought you had done previously.<br>
<br>
The difference in the coordinate file vs. topology is 30 atoms,<br>
which is more than both of your ligands (20 atoms), so your problem<br>
likely lies elsewhere.<br>
<br>
-Justin<br>
<br>
<br>
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>
-- Ahmet YILDIRIM<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
</div></blockquote><div><div></div><div class="h5">
<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 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>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>