[gmx-users] protein-ligand complex tutorial
Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 19 00:29:05 CEST 2011
ahmet yıldırım wrote:
> Dear Justin,
>
> If I send your e-mail the conf.gro, topol.top and PO4.itp files, can you
> look at them? do you have a little time?
>
There are many problems with the files you sent me.
1. The [molecules] section in no way reflects the contents of the system. You have:
[ molecules ]
; Compound #mols
Protein_chain_A 1
PO4 2
SOL 220
SOL 15025
There are two things wrong here: (a) you have only 220 molecules of water, so
the second SOL block refers to something that doesn't exist and (b) as I have
said several times now, the molecules are listed out of order. In the .gro
file, your two PO4 molecules are listed last, after the protein and water. In
the topology, they follow the protein, but are listed before the water. The
order of the molecules in the coordinate file and [molecules] listing must match
exactly.
2. The spacing of the lines in conf.gro for PO4 is still wrong. Please make
sure to read this message in monospace font so it is clear. You have:
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
The PO4 lines need to be adjusted so that the residue names are aligned
properly, i.e.:
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
The required .gro file format is discussed in the online manual. You must
adhere to it for proper interpretation:
http://manual.gromacs.org/online/gro.html
After making these changes, grompp stops complaining.
-Justin
>
>
> 19 Nisan 2011 00:59 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
>
> ahmet yıldırım wrote:
>
> Dear Justin,
>
> I rearranged conf.gro but Gromacs is giving the same errors
> again. I think I am going mad :-(
>
>
> In the absence of the corresponding topology, there is no way to
> help you other than to say you're still doing something wrong.
>
> Your coordinates still appear misaligned. I can confirm that the
> spacing errors will lead to incorrect coordinate interpretation and
> thus the warning about the charge groups.
>
> -Justin
>
> *_conf.gro_*
>
> 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
> 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750
> 0.00000 0.00000 0.00000
>
> 19 Nisan 2011 00:37 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>> yazdı:
>
>
>
>
> 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>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
> <mailto: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>>>
> <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
> <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> <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
> <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>>>
> <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 <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>
> <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 <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> <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> <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> <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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