Dear Justin,<br><br>without_JZ4_PO4_BME.pdb ( There arent ligands)<br>1.pdb2gmx -f without_JZ4_PO4_BME.pdb<br>forcefield:43a1, water:spc<br>Now I have topol.top and conf.gro files.<br>2.I have "PO4.gro" and" PO4.itp" from PRODRG using the following all lines.<br>
HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P <br>HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O <br>HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O <br>
HETATM 1369 O3 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 11.36 O <br>HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P <br>
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O <br>HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O <br>HETATM 1374 O3 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 15.77 O <br><br>3. I added 5 atoms/lines into the conf.gro file from PO4.gro and 5 the second line of conf.gro.<br>4. I added to topol.top the following lines:<br>
; Include ligand topology<br><b><span style="color: rgb(153, 0, 0);">#include "PO4.itp"</span></b><br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br><b style="color: rgb(153, 0, 0);">PO4 2</b><br>
SOL 220<br>5. editconf -f conf.gro -bt cubic -d 1.0 -o box.gro<br>6. genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro<br>7. grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br><b style="color: rgb(153, 0, 0);">Fatal Error:</b><br>
number of coordinates in coordinate file (solvated.gro, 47439)<br> does not match topology (topol.top, 47444)<br><br><br><br><div class="gmail_quote">2011/4/18 lucioric <span dir="ltr"><<a href="mailto:lucioric@ibt.unam.mx">lucioric@ibt.unam.mx</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;">You need to get or calculate parameters for phosphate. These parameters are yet calculated for the AMBER forcefield, there are in <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>. You need to install AmberTools and copy the frcmod.phos file in the URL above to the appropriate directory (see the AmberTools manual). Then, you can build the topology and coordinate files in AMBER format for your system using the tleap tool. These files in AMBER format can be converted to Gromacs format using the acpype program. With these files in Gromacs format you can run a MD in Gromacs, using the Amber forcefield.<br>
Lucio Montero<br>
Instituto de Biotecnologia, UNAM, Mexico.<div><div></div><div class="h5"><br>
On Mon, 18 Apr 2011 20:40:49 +0300, ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>> 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>
You prepared a useful tutorial. if you used PO4 ligand (which has 2<br>
molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and<br>
.gro files of ligand because of 2 molecule, what 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 13.01 P<br>
HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O<br>
HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O<br>
<br>
HETATM 1369 O3 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 11.36 O<br>
HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P<br>
HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O<br>
<br>
HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O<br>
HETATM 1374 O3 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 15.77 O<br>
HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C<br>
<br>
..<br>
</blockquote>
<br>
-- <br></div></div><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>