[gmx-users] adding new atoms in .itp file
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 22 20:28:31 CET 2005
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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>>
>>
>>
>> --
>> 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".
>
>
>
>
> --
> 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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