[gmx-users] adding new atoms in .itp file
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 22 20:24:20 CET 2005
Viswanadham Sridhara 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.
This is most likely the problem. You may have overlapping atoms.
> 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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> >
> >
> >
> >
> > --
> > 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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