[gmx-users] adding new atoms in .itp file
David van der Spoel
spoel at xray.bmc.uu.se
Sat Dec 24 21:31:59 CET 2005
Viswanadham Sridhara wrote:
> 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.
please check carefully that the protein really has 1343 atoms in your
gro and top file, and if that is the case make a new index file using
make_ndx.
It seems like you have mixed up some files with and without HE1
> Thanks and Merrry X-mas to everyone,
> Vissu
>
> On 12/22/05, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto: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>
> > <mailto: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>
> > <mailto: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>>
> >> <mailto: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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> <mailto:gmx-users at gromacs.org> <mailto: gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
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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>>
> >> <mailto: 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>>
> >> <mailto: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".
> >>
> >>------------------------------------------------------------------------
> >
> >>
> >>_______________________________________________
> >>gmx-users mailing list
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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
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> >
> >
> > _______________________________________________
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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
> <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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>
>
>
>
> --
> 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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