[gmx-users] protein-ligand complex tutorial
ahmet yıldırım
ahmedo047 at gmail.com
Mon Apr 18 23:02:31 CEST 2011
Dear Justin,
Now, I added two PO4 to the coordinate file, then added two to the topology.
I created PO4_1.gro and PO4_1.itp for first PO4 using PRODRG. Then, I
created PO4_2.gro and PO4_2.itp for first PO4 using PRODRG. I added 10
atoms/lines into conf.gro from PO4.gro(5cordinate and PO4_2.gro files (5
coordinate), then 10 the second line of conf.gro. I used only one because of
the same as PO4_1.itp and PO4_2.itp files.
*First PO4 from 3HTB:*
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
*second PO4 from 3HTB:*
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
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*WARNING 1* [file topol.top, line 10673]:
670 non-matching atom names
atom names from topol.top will be used
atom names from solvated.gro will be ignored
*WARNING 2* [file em.mdp]:
The sum of the two largest charge group radii (7.005889) is larger than
rlist (1.000000
*NOTE 1* [file topol.top, line 10673]:
System has non-zero total charge: 2.000001e+00
*Fatal error:*
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
18 Nisan 2011 23:26 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
> 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
>>
>> ..
>>
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>>
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110419/926d6a12/attachment.html>
More information about the gromacs.org_gmx-users
mailing list