[gmx-users] protein-ligand complex tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 18 23:59:43 CEST 2011



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>> 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>>> 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>>>> 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>>>>>
> 
> 
> 
>                          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>>>>> 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> | (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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