Dear Justin,<br><br>I rearranged conf.gro but Gromacs is giving the same errors again. I think I am going mad :-(<br><b><u>conf.gro</u></b><br>388HOH HW2 2353 1.763 -1.939 1.371<br> 1PO4 O2 1 1.456 -2.557 1.128<br>
1PO4 P 2 1.543 -2.651 1.204<br> 1PO4 O3 3 1.507 -2.801 1.181<br> 1PO4 O4 4 1.504 -2.632 1.354<br> 1PO4 O1 5 1.690 -2.636 1.176<br> 1PO4 O2 1 2.196 0.201 -1.915<br>
1PO4 P 2 2.174 0.062 -1.865<br> 1PO4 O3 3 2.062 -0.001 -1.948<br> 1PO4 O4 4 2.142 0.066 -1.713<br> 1PO4 O1 5 2.307 -0.006 -1.892<br> 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000<br>
<br><div class="gmail_quote">19 Nisan 2011 00:37 tarihinde Justin A. Lemkul <span dir="ltr"><<a 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">
But I doesn't see any error in the conf.gro. Am I wrong?<br>
_conf.gro:_<br>
LYSOZYME<br>
2363<br>
1MET N 1 0.556 -1.596 -0.893<br>
...<br>
388HOH HW2 2353 1.763 -1.939 1.371<br>
1PO4 O2 1 1.456 -2.557 1.128<br>
1PO4 P 2 1.543 -2.651 1.204<br>
1PO4 O3 3 1.507 -2.801 1.181<br>
1PO4 O4 4 1.504 -2.632 1.354<br>
1PO4 O1 5 1.690 -2.636 1.176<br>
1PO4 O2 1 2.196 0.201 -1.915<br>
1PO4 P 2 2.174 0.062 -1.865<br>
1PO4 O3 3 2.062 -0.001 -1.948<br>
1PO4 O4 4 2.142 0.066 -1.713<br>
1PO4 O1 5 2.307 -0.006 -1.892<br>
</div></blockquote>
<br>
Well, if my monospace font is any indication, yes, you have column misalignment in the coordinates that could be causing a problem regarding charge group size. I also don't know if the identical residue number will cause a problem between your two PO4 molecules, but it might.<br>
<br>
The other issue about mismatched atom names is a combination of the coordinate file and topology not agreeing with respect to their order.<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;"><div class="im">
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000<br>
<br></div>
19 Nisan 2011 00:12 tarihinde 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>>> yazdı:<div><div>
</div><div class="h5"><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear Justin,<br>
<br>
Now, I added two PO4 to the coordinate file, then added two to<br>
the topology. I created PO4_1.gro and PO4_1.itp for first PO4<br>
using PRODRG. Then, I created PO4_2.gro and PO4_2.itp for first<br>
PO4 using PRODRG. I added 10 atoms/lines into conf.gro from<br>
PO4.gro(5cordinate and PO4_2.gro files (5 coordinate), then 10<br>
the second line of conf.gro. I used only one because of the same<br>
as PO4_1.itp and PO4_2.itp files.<br>
<br>
<br>
That's exactly what you want to do - an .itp defines a<br>
[moleculetype]. If you have two identical molecules that are<br>
defined by the same [moleculetype], you don't want to #include the<br>
same thing twice. In fact, grompp will throw a fatal error that<br>
your [moleculetype] is redefined. Think of this analogy - you<br>
#include "spc.itp" in your system, but you don't do it for every<br>
single water molecule individually. You define the [moleculetype]<br>
and then define in the topology how many instances of that<br>
particular molecule in the [molecules] directive.<br>
<br>
*_First PO4 from 3HTB:_*<br>
<br>
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70<br>
13.01 P HETATM 1367 O1 PO4 A 165 16.899 -26.359<br>
11.761 0.70 8.42 O HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O HETATM 1369 O3<br>
PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O<br>
HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70<br>
11.36 O<br>
*_second PO4 from 3HTB:_*<br>
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50<br>
20.49 P HETATM 1372 O1 PO4 A 166 23.073 -0.065<br>
-18.917 0.50 18.04 O HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O HETATM 1374 O3<br>
PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O<br>
HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50<br>
15.77 O<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>
*WARNING 1* [file topol.top, line 10673]:<br>
670 non-matching atom names<br>
atom names from topol.top will be used<br>
atom names from solvated.gro will be ignored<br>
<br>
<br>
As I said in my last message, the order of the contents of the<br>
coordinate file and [molecules] directive must match. You have not<br>
satisfied this requirement.<br>
<br>
*WARNING 2* [file em.mdp]:<br>
<br>
The sum of the two largest charge group radii (7.005889) is<br>
larger than<br>
rlist (1.000000<br>
<br>
<br>
I have no idea what might cause this other than you've mangled the<br>
coordinates in some way, or perhaps molecules are broken across<br>
periodic boundaries. In a normal input file, the latter is not the<br>
case. My guess is that your copying/pasting of coordinates is<br>
somehow at fault.<br>
<br>
-Justin<br>
<br>
*NOTE 1* [file topol.top, line 10673]:<br>
<br>
System has non-zero total charge: 2.000001e+00<br>
*Fatal error:*<br>
Too many warnings (2), grompp terminated.<br>
If you are sure all warnings are harmless, use the -maxwarn option.<br>
<br>
<br>
<br>
<br>
18 Nisan 2011 23:26 tarihinde Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div></div>
<mailto:<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 class="im"><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> yazdı:<br>
<br>
<br>
<br>
You said you added one PO4 to the coordinate file, but then added<br>
two to the topology. Hence the difference of exactly 5 atoms, or<br>
one PO4 molecule.<br>
<br>
The content of the coordinate file must always match the<br>
content of<br>
the topology, with respect to the number of atoms (based on the<br>
listing of molecules) and the order in which they appear in the<br>
[molecules] directive.<br>
<br>
-Justin<br>
<br>
<br>
<br>
2011/4/18 lucioric <<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a><br>
<mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a>><br>
<mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a><br></div>
<mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a>>> <mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a><div class="im"><br>
<mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a>><br>
<br></div>
<mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a> <mailto:<a href="mailto:lucioric@ibt.unam.mx" target="_blank">lucioric@ibt.unam.mx</a>>>>><div><div>
</div><div class="h5"><br>
<br>
<br>
You need to get or calculate parameters for phosphate.<br>
These<br>
parameters are yet calculated for the AMBER<br>
forcefield, there<br>
are in<br>
<a href="http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos" target="_blank">http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos</a>.<br>
You need to install AmberTools and copy the<br>
frcmod.phos file<br>
in the<br>
URL above to the appropriate directory (see the AmberTools<br>
manual).<br>
Then, you can build the topology and coordinate files<br>
in AMBER<br>
format for your system using the tleap tool. These<br>
files in AMBER<br>
format can be converted to Gromacs format using the acpype<br>
program.<br>
With these files in Gromacs format you can run a MD in<br>
Gromacs,<br>
using the Amber forcefield.<br>
Lucio Montero<br>
Instituto de Biotecnologia, UNAM, Mexico.<br>
<br>
On Mon, 18 Apr 2011 20:40:49 +0300, ahmet yıldırım<br>
<<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>><br>
<mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>><br>
<mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>><br>
<mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>>>> wrote:<br>
<br>
Dear Justin,<br>
<br>
You prepared a useful tutorial. if you used PO4 ligand<br>
(which has 2<br>
molecule) instead of 1JZ4 ligand from 3HTB.pdb,<br>
Then, in the<br>
.itp and<br>
.gro files of ligand because of 2 molecule, what<br>
change?<br>
Can you give some hint?<br>
Thanks<br>
<br>
3HTB.pdb<br>
....<br>
<br>
TER 1365 ASN A 163<br>
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70<br>
13.01 P<br>
HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761<br>
0.70 8.42 O<br>
HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281<br>
0.70 12.47 O<br>
<br>
HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811<br>
0.70 11.58 O<br>
HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543<br>
0.70 11.36 O<br>
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50<br>
20.49 P<br>
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917<br>
0.50 18.04 O<br>
<br>
HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50<br>
19.25 O<br>
HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484<br>
0.50 14.22 O<br>
HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50<br>
15.77 O<br>
HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071<br>
1.00 16.39 C<br>
<br>
..<br>
<br>
<br>
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-- 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>
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<br>
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-- ========================================<br>
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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>
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</div></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>
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