[gmx-users] protein-ligand complex tutorial
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 18 23:37:02 CEST 2011
ahmet yıldırım wrote:
> Dear Justin,
>
> But I doesn't see any error in the conf.gro. Am I wrong?
> _conf.gro:_
> LYSOZYME
> 2363
> 1MET N 1 0.556 -1.596 -0.893
> ...
> 388HOH HW2 2353 1.763 -1.939 1.371
> 1PO4 O2 1 1.456 -2.557 1.128
> 1PO4 P 2 1.543 -2.651 1.204
> 1PO4 O3 3 1.507 -2.801 1.181
> 1PO4 O4 4 1.504 -2.632 1.354
> 1PO4 O1 5 1.690 -2.636 1.176
> 1PO4 O2 1 2.196 0.201 -1.915
> 1PO4 P 2 2.174 0.062 -1.865
> 1PO4 O3 3 2.062 -0.001 -1.948
> 1PO4 O4 4 2.142 0.066 -1.713
> 1PO4 O1 5 2.307 -0.006 -1.892
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.
The other issue about mismatched atom names is a combination of the coordinate
file and topology not agreeing with respect to their order.
-Justin
> 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000
> 0.00000 0.00000
>
> 19 Nisan 2011 00:12 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
>
> ahmet yıldırım wrote:
>
> 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.
>
>
> That's exactly what you want to do - an .itp defines a
> [moleculetype]. If you have two identical molecules that are
> defined by the same [moleculetype], you don't want to #include the
> same thing twice. In fact, grompp will throw a fatal error that
> your [moleculetype] is redefined. Think of this analogy - you
> #include "spc.itp" in your system, but you don't do it for every
> single water molecule individually. You define the [moleculetype]
> and then define in the topology how many instances of that
> particular molecule in the [molecules] directive.
>
> *_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
>
>
> As I said in my last message, the order of the contents of the
> coordinate file and [molecules] directive must match. You have not
> satisfied this requirement.
>
> *WARNING 2* [file em.mdp]:
>
> The sum of the two largest charge group radii (7.005889) is
> larger than
> rlist (1.000000
>
>
> I have no idea what might cause this other than you've mangled the
> coordinates in some way, or perhaps molecules are broken across
> periodic boundaries. In a normal input file, the latter is not the
> case. My guess is that your copying/pasting of coordinates is
> somehow at fault.
>
> -Justin
>
> *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
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto: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>
> <mailto:lucioric at ibt.unam.mx
> <mailto:lucioric at ibt.unam.mx>> <mailto:lucioric at ibt.unam.mx
> <mailto:lucioric at ibt.unam.mx>
>
> <mailto: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>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>
> <mailto: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 <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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