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

[David van der Spoel]

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
>     > --
>     >
>     >------------------------------------------------------------------------
>
>     >
>     >_______________________________________________
>     >gmx-users mailing list
>     >gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     > http://www.gromacs.org/mailman/listinfo/gmx-users
>     >Please don't post (un)subscribe requests to the list. Use the
>     >www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     >
>
>
>     --
>     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
>     <http://xray.bmc.uu.se/%7Espoel>
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>     _______________________________________________
>     gmx-users mailing list
>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>
>
>
>
> -- 
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
>------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++