[gmx-users] protein-ligand complex tutorial
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 18 22:26:23 CEST 2011
ahmet yıldırım wrote:
> Dear Justin,
>
> without_JZ4_PO4_BME.pdb ( There arent ligands)
> 1.pdb2gmx -f without_JZ4_PO4_BME.pdb
> forcefield:43a1, water:spc
> Now I have topol.top and conf.gro files.
> 2.I have "PO4.gro" and" PO4.itp" from PRODRG using the following all lines.
> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70
> 13.01 P
> HETATM 1367 O1 PO4 A 165 16.899 -26.359 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 PO4 A 165 15.071 -28.010 11.811 0.70
> 11.58 O
> HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70
> 11.36 O
> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50
> 20.49 P
> HETATM 1372 O1 PO4 A 166 23.073 -0.065 -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 PO4 A 166 20.616 -0.014 -19.484 0.50
> 14.22 O
> HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50
> 15.77 O
>
> 3. I added 5 atoms/lines into the conf.gro file from PO4.gro and 5 the
> second line of conf.gro.
> 4. I added to topol.top the following lines:
> ; Include ligand topology
> *#include "PO4.itp"*
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> *PO4 2*
> SOL 220
> 5. editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
> 6. genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> 7. grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> *Fatal Error:*
> number of coordinates in coordinate file (solvated.gro, 47439)
> does not match topology (topol.top, 47444)
>
You said you added one PO4 to the coordinate file, but then added two to the
topology. Hence the difference of exactly 5 atoms, or one PO4 molecule.
The content of the coordinate file must always match the content of the
topology, with respect to the number of atoms (based on the listing of
molecules) and the order in which they appear in the [molecules] directive.
-Justin
>
>
> 2011/4/18 lucioric <lucioric at ibt.unam.mx <mailto:lucioric at ibt.unam.mx>>
>
> You need to get or calculate parameters for phosphate. These
> parameters are yet calculated for the AMBER forcefield, there are in
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos.
> 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.
> Lucio Montero
> Instituto de Biotecnologia, UNAM, Mexico.
>
> On Mon, 18 Apr 2011 20:40:49 +0300, ahmet yıldırım
> <ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>> wrote:
>
> Dear Justin,
>
> You prepared a useful tutorial. if you used PO4 ligand (which has 2
> molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the
> .itp and
> .gro files of ligand because of 2 molecule, what change?
> Can you give some hint?
> Thanks
>
> 3HTB.pdb
> ....
>
> TER 1365 ASN A 163
> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P
> HETATM 1367 O1 PO4 A 165 16.899 -26.359 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 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O
> HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O
> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P
> HETATM 1372 O1 PO4 A 166 23.073 -0.065 -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 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O
> HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O
> HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C
>
> ..
>
>
> --
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>
>
> --
> Ahmet YILDIRIM
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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