Re: [gmx-users] protein-ligand complex tutorial

[Justin A. Lemkul]

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 <jalem...@vt.edu 
<mailto:jalem...@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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>

               <mailto:jalem...@vt.edu <mailto:jalem...@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 <lucio...@ibt.unam.mx
        <mailto:lucio...@ibt.unam.mx>
               <mailto:lucio...@ibt.unam.mx <mailto:lucio...@ibt.unam.mx>>
                      <mailto:lucio...@ibt.unam.mx
        <mailto:lucio...@ibt.unam.mx>
               <mailto:lucio...@ibt.unam.mx
        <mailto:lucio...@ibt.unam.mx>>> <mailto:lucio...@ibt.unam.mx
        <mailto:lucio...@ibt.unam.mx>

               <mailto:lucio...@ibt.unam.mx <mailto:lucio...@ibt.unam.mx>>

                      <mailto:lucio...@ibt.unam.mx
        <mailto:lucio...@ibt.unam.mx> <mailto:lucio...@ibt.unam.mx
        <mailto:lucio...@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
                         <ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com>>
               <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>
        <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>>
                      <mailto:ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com> <mailto:ahmedo...@gmail.com
        <mailto:ahmedo...@gmail.com>>
               <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>
        <mailto:ahmedo...@gmail.com <mailto:ahmedo...@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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