[gmx-users] protein-ligand complex tutorial

ahmet yıldırım ahmedo047 at gmail.com
Mon Apr 18 20:37:05 CEST 2011


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)



2011/4/18 lucioric <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>
> 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
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