[gmx-users] adding new atoms in .itp file

Viswanadham Sridhara muta.mestri at gmail.com
Thu Dec 22 20:24:19 CET 2005


Just a continuation of my previous email, I was wondering how the
interactions between protein and lipid bilayer are included, should I put
the option "yes" in generate pairs in ffgmx.itp or how does it work? I know
its a naive question though....
Thanks,


On 12/22/05, Viswanadham Sridhara <muta.mestri at gmail.com> wrote:
>
> Hi David,
> I did with -inter option and it worked, now I got the itp file for
> protein.
> And I have taken dppc bilayer from Dr.Tieleman's website, and I inserted
> protein in bilayer.
> Now my question is, should my topology file look like this:
> #include "ffgmx.itp"
> #include "protein.itp"
> #include "dppc.itp".......and so on.
> I got an error while running energy minimisation,
> it ended saying fmax norm is infinity on one atom, should I do any other
> steps in between, am using flexible water for EM.
> Thanks in advance,
> Vissu
>
>
>  On 12/21/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> >
> > Viswanadham Sridhara wrote:
> >
> > > The only problem with my pdb file is that it has 1330 atoms, I think I
> >
> > > cant use prodrg with more than 300.......
> > > As you pointed out, I will try to make a decent pdb file.
> > >
> > > One more question,
> > > This is a part of my .itp file
> > >
> > > 295          N     40    GLU      N    206      - 0.28    14.0067   ;
> > > qtot -1.28
> > >    296          H     40    GLU      H    206       0.28      1.008
> > > ; qtot -1
> > >    297        CH1     40    GLU     CA    207          0     13.019
> > > ; qtot -1
> > >    298        CH2     40    GLU     CB    208          0     14.027
> > > ; qtot -1
> > >    299        CH2     40    GLU     CG    209          0     14.027
> > > ; qtot -1
> > >    300          C     40    GLU     CD    210       0.27     12.011
> > > ; qtot -0.73
> > >    301         OM     40    GLU    OE1    210     -0.635    15.9994
> > > ; qtot -1.365
> > >    302         OM     40    GLU    OE2    210     -0.635    15.9994
> > > ; qtot -2
> > >    303          C     40    GLU      C    211       0.38     12.011
> > > ; qtot -1.62
> > >    304          O     40    GLU      O    211      -0.38    15.9994
> > > ; qtot -2
> > >
> > > while in pdb file,
> > >
> > > ATOM    295  N   GLU    40      20.250  25.090  41.950  1.00  0.00
> > > ATOM    296  H   GLU    40      20.340  25.930  41.420  1.00  0.00
> > > ATOM    297  CA  GLU    40      20.620  25.440  43.320   1.00  0.00
> > > ATOM    298  CB  GLU    40      21.210  26.840  43.440  1.00  0.00
> > > ATOM    299  CG  GLU    40      22.630  26.980  42.910  1.00  0.00
> > > ATOM    300  CD  GLU    40      23.050  28.450  42.940   1.00  0.00
> > > ATOM    301  OE1 GLU    40      22.680  29.310  42.130  1.00  0.00
> > > ATOM    302  OE2 GLU    40      23.780  28.750  44.050  1.00  0.00
> > > ATOM    303  HE2 GLU    40      24.010  29.710  43.890   1.00  0.00
> > > ATOM    304  C   GLU    40      19.560  25.240  44.400  1.00  0.00
> > > ATOM    305  O   GLU    40      19.800  24.810  45.530  1.00  0.00
> > >
> > > if you can see, HE2 is missing in .itp file, when i used pdb2gmx
> > > program, this might be due to its description in ffgmx.rtp file which
> > is
> > > [ GLU ]
> > >  [ atoms ]
> > >      N     N  -0.280     0
> > >      H     H   0.280     0
> > >     CA   CH1   0.000     1
> > >     CB   CH2   0.000     2
> > >     CG   CH2   0.000     3
> > >     CD     C   0.270     4
> > >    OE1    OM  -0.635     4
> > >    OE2    OM  -0.635     4
> > >      C     C   0.380     5
> > >      O     O  - 0.380     5
> > >
> > > %%%%%%%%%%%
> > > Should I add that atom type in .rtp file, or is there any other way
> > > pdb2gmx can take care of this.
> >
> >
> > No, you should run pdb2gmx -inter and select GLUH for the residue in
> > question. This will put the proton on OE1, but that should still give
> > the same effect.
> >
> > > Thanks in advance,
> > > Vissu
> > >
> > >
> > > On 12/21/05, *David van der Spoel* < spoel at xray.bmc.uu.se
> > > <mailto:spoel at xray.bmc.uu.se>> wrote:
> > >
> > >     Viswanadham Sridhara wrote:
> > >
> > >     >
> > >     > Hi Everyone,
> > >     > I have a .itp file, where I want to add new atoms in between, is
> > >     there
> > >     > any way that I can add them at the end, but give the respective
> > >     > residue number, or should they be in order and represent .pdb
> > file.
> > >
> > >
> > >     Not easy (ch. 5). Try other means, maybe prodrg, or make a good
> > >     pdb file
> > >     from it (if it is a protein).
> > >
> > >     > Thanks,
> > >     > -Vissu
> > >     > --
> > >     >
> > >
> > >------------------------------------------------------------------------
> > >
> > >     >
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> > >
> > >
> > >     --
> > >     David.
> > >
> > ________________________________________________________________________
> > >     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
> > group,
> > >     Dept. of Cell and Molecular Biology, Uppsala University.
> > >     Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > >     phone:  46 18 471 4205          fax: 46 18 511 755
> > >     spoel at xray.bmc.uu.se
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> > >
> > >
> > >
> > > --
> > > Viswanadham Sridhara,
> > > Graduate Research Assistant,
> > > Old Dominion University, "VIRGINIA".
> > >
> >
> > >------------------------------------------------------------------------
> > >
> > >_______________________________________________
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> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se     spoel at gromacs.org
> > http://xray.bmc.uu.se/~spoel
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>
>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>



--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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