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

Viswanadham Sridhara muta.mestri at gmail.com
Sat Dec 24 21:16:01 CET 2005


Everything went fine at this point. Thanks David.

My protein has 1343 atoms in it, but when I try to make an index file, it is
going from 1 - 1336, the only reason i can think is when I use -inter
option, I protonated 7 OE2 in GLU residue, so the difference of 1343 and
1336. But dont you think , the index file of protein should run from 1-1343
and then the bilayer indices start.
In my case, the index file of the bilayer is starting from 1337, while in
the pdb file, it is from 1344, should I manually change them?? I hope yes.
Thanks and Merrry X-mas to everyone,
Vissu

On 12/22/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Viswanadham Sridhara wrote:
> > 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....
> Not naive, but it is written in the manual. Anyway, the parameters are
> already in ffgmx.itp
>
> > Thanks,
> >
> >
> > On 12/22/05, *Viswanadham Sridhara* <muta.mestri at gmail.com
> > <mailto: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
> >     <mailto: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>
> >>  <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> >>     <mailto:spoel at xray.bmc.uu.se
> >         <mailto:spoel at xray.bmc.uu.se>>     spoel at gromacs.org
> >         <mailto:spoel at gromacs.org>
> >>     <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
> >         http://xray.bmc.uu.se/~spoel
> >>     <http://xray.bmc.uu.se/%7Espoel
> >         <http://xray.bmc.uu.se/%7Espoel>>
> >>
> >
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> >
> >>
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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 <mailto:spoel at xray.bmc.uu.se>
> >         spoel at gromacs.org <mailto:spoel at gromacs.org>
> >         http://xray.bmc.uu.se/~spoel
> >
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> >
> >
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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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>
> --
> 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".
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