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

[Viswanadham Sridhara]

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.
Thanks in advance,
Vissu


On 12/21/05, David van der Spoel <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.
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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