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On 16/04/2011 6:05 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:BANLkTi=iZ+tUX0p7FPNCGGhjg+9s3e+fpA@mail.gmail.com"
type="cite">Dear Justin,<br>
<br>
I have 6 EDO and 1 TRS ligans. I created <span id="result_box"
class="short_text" lang="en"><span title="Alternatif çevirileri
görmek için tıklayın" class="hps">coordinate</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">and</span>
.itp files <span title="Alternatif çevirileri görmek için
tıklayın" class="hps">for</span> <span title="Alternatif
çevirileri görmek için tıklayın" class="hps">each</span> EDO <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">molecule</span><span
class="" title="Alternatif çevirileri görmek için tıklayın"> </span></span>using
prodrg web server. Then I created 6 .itp files as EDO1.itp,
EDO2.itp.....EDO6.itp.</blockquote>
<br>
Why? The fragment<br>
<br>
[molecules]<br>
EDO 6<br>
<br>
is what specifies six identical EDO molecules.<br>
<br>
Your earlier problem was in matching the contents of your
[molecules] section with your coordinate file. They have to contain
the same molecules in the same order.<br>
<br>
<blockquote
cite="mid:BANLkTi=iZ+tUX0p7FPNCGGhjg+9s3e+fpA@mail.gmail.com"
type="cite"> I changed residue numbers. But I have Fatal Error
"moleculetype EDO is redefined". <span id="result_box"
class="short_text" lang="en"><span title="Alternatif çevirileri
görmek için tıklayın" class="hps">Am</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">I</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">on the wrong track?:-(</span></span><br>
</blockquote>
<br>
So don't re-define moleculetype EDO.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=iZ+tUX0p7FPNCGGhjg+9s3e+fpA@mail.gmail.com"
type="cite">
<br>
<u><b>EDO1.itp:</b></u><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 O1 1 -0.163 15.9994 <br>
2 H 1 EDO HAA 1 0.074 1.0080 <br>
3 CH2 1 EDO C1 1 0.089 14.0270 <br>
4 CH2 1 EDO C2 2 0.089 14.0270 <br>
5 OA 1 EDO O2 2 -0.163 15.9994 <br>
6 H 1 EDO HAB 2 0.074 1.0080 <br>
<br>
<b><u>EDO2.itp:</u></b><br>
[ moleculetype ]<br>
; Name nrexcl<br>
EDO 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 2 EDO O1 1 -0.163 15.9994 <br>
2 H 2 EDO HAA 1 0.074 1.0080 <br>
3 CH2 2 EDO C1 1 0.089 14.0270 <br>
4 CH2 2 EDO C2 2 0.089 14.0270 <br>
5 OA 2 EDO O2 2 -0.163 15.9994 <br>
6 H 2 EDO HAB 2 0.074 1.0080 <br>
<u><b>topol.top</b></u>:<br>
...<br>
#include "EDO1.itp"<br>
#include "EDO2.itp"<br>
#include "EDO3.itp"<br>
#include "EDO4.itp"<br>
#include "EDO5.itp"<br>
#include "EDO6.itp"<br>
#include "TRS.itp"<br>
...<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
EDO 6<br>
TRS 1<br>
SOL 185<br>
SOL 143<br>
SOL 33713<br>
<br>
<u><b>conf.gro:</b></u><br>
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br>
5384<br>
2GLN N 1 1.458 -1.158 0.739<br>
2GLN H1 2 1.520 -1.083 0.763<br>
....<br>
<br>
485HOH HW1 5333 0.221 -3.864 -2.291<br>
485HOH HW2 5334 0.303 -3.946 -2.407<br>
1EDO O1 1 0.625 -3.071 -0.171<br>
1EDO HAA 2 0.698 -3.048 -0.107<br>
1EDO C1 3 0.596 -3.211 -0.163<br>
1EDO C2 4 0.486 -3.247 -0.261<br>
1EDO O2 5 0.365 -3.179 -0.224<br>
1EDO HAB 6 0.292 -3.203 -0.288<br>
2EDO O1 1 2.023 -4.300 0.220<br>
2EDO HAA 2 2.046 -4.296 0.317<br>
2EDO C1 3 2.138 -4.342 0.146<br>
2EDO C2 4 2.096 -4.347 -0.001<br>
2EDO O2 5 2.196 -4.412 -0.079<br>
2EDO HAB 6 2.167 -4.415 -0.174<br>
3EDO O1 1 2.502 -3.407 -2.265<br>
3EDO HAA 2 2.529 -3.365 -2.178<br>
3EDO C1 3 2.466 -3.303 -2.359<br>
3EDO C2 4 2.424 -3.364 -2.492<br>
3EDO O2 5 2.294 -3.423 -2.477<br>
3EDO HAB 6 2.265 -3.464 -2.564<br>
4EDO O1 1 1.021 -5.733 -2.007<br>
4EDO HAA 2 0.952 -5.780 -2.061<br>
4EDO C1 3 0.995 -5.753 -1.868<br>
4EDO C2 4 1.102 -5.679 -1.787<br>
4EDO O2 5 1.091 -5.540 -1.816<br>
4EDO HAB 6 1.160 -5.489 -1.764<br>
5EDO O1 1 1.988 -3.117 -3.247<br>
5EDO HAA 2 1.915 -3.177 -3.217<br>
5EDO C1 3 2.100 -3.194 -3.291<br>
5EDO C2 4 2.212 -3.102 -3.337<br>
5EDO O2 5 2.247 -3.012 -3.231<br>
5EDO HAB 6 2.321 -2.952 -3.261<br>
6EDO O1 1 0.987 -4.579 -0.020<br>
6EDO HAA 2 0.969 -4.622 -0.109<br>
6EDO C1 3 1.118 -4.521 -0.021<br>
6EDO C2 4 1.145 -4.456 0.114<br>
6EDO O2 5 1.054 -4.506 0.212<br>
6EDO HAB 6 1.073 -4.463 0.300<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>
<div class="gmail_quote">14 Nisan 2011 21:09 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;">
<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 Justin,<br>
<br>
<div class="im">
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>
</div>
</blockquote>
<br>
Well, it's certainly not working, is it? You only have one
EDO molecule shown here. Is this the only one? If it is,
then you need to build the system to reflect what you actually
want to do. No one on this list can tell you that. You have
to build a starting configuration that fits the goals of your
study.<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;">
_*conf.gro:*_
<div>
<div class="h5"><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>
</div>
14 Nisan 2011 20:15 tarihinde Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>>> yazdı:
<div>
<div>
</div>
<div class="h5"><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear Justin,<br>
<br>
I built .rtp entries for two ligands using<br>
(<a moz-do-not-send="true"
href="http://davapc1.bioch.dundee.ac.uk/prodrg/"
target="_blank">http://davapc1.bioch.dundee.ac.uk/prodrg/</a>).
I added to the<br>
topol.top the following parts:<br>
#include "TRS.itp"<br>
#include "EDO.itp"<br>
<br>
<br>
Well, either pdb2gmx built the molecules into your
topology or<br>
you're #including them in this manner, you should not
do both.<br>
<br>
TRS 1<br>
EDO 6<br>
<br>
<br>
So this is part of your [molecules] directive? If
you've got six<br>
copies of EDO, that's likely where the disconnect
comes from - you<br>
only had one in your previous coordinate file
snippet.<br>
<br>
<br>
Furthermore I added the number of atoms (20) in
the second line<br>
of the<br>
<br>
<br>
If you have 6 EDO, the necessary addition is more
than just 20.<br>
<br>
<br>
.gro file. may the problem related to pdb file
(3NM4.pdb)?<br>
Because -OH groups seems as -O. isn't it? maybe
I'm wrong. What<br>
would you recommend?<br>
<br>
<br>
Generally H atoms are not present in crystal
structures. If your<br>
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<br>
and run pdb2gmx.<br>
<br>
2. Have no H atoms present in the initial coordinate
file and build<br>
suitable .hdb entries for your ligands so they will
be constructed<br>
from existing atoms.<br>
<br>
It seems like you're applying several different
methods at once.<br>
There are protein-ligand tutorials that you may find
useful for<br>
keeping all of this straight (I recommend my own):<br>
<br>
<a moz-do-not-send="true"
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>
2011/4/14 Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a><br>
</div>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<div>
<div class="h5"><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>><br>
<br>
<br>
<br>
<br>
ahmet yıldırım 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<br>
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,<br>
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<br>
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<br>
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<br>
conf.gro<br>
file you show below is indeed what you used,
though, I see no<br>
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<br>
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<br>
-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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> | (540)
<div class="im">
<br>
231-9080<br>
<br>
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href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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<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>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> <<a
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<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
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href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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<br>
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-- <br>
Ahmet YILDIRIM<br>
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