[gmx-users] Chage modifications with pdb2gmx

[Krzeminski]

On Tuesday 06 September 2005 08:52, David van der Spoel wrote:
> On Mon, 2005-09-05 at 20:45 +0200, Krzeminski wrote:
> > Hi Gromacs users,
> >
> > I tried to find the solution of this problem in the forum, but I did not
> > manage...
> >
> > Actually, I created a new building block for a residue in the rtp file.
> > This following is an extract of this residue:
>
> have you modified the hdb file too?
Of course... This is the extract that deals with the new residue:

GNP     6
        1       1       N3B      PB      PG
        1       2       O3G      PG     N3B
        2       3        N2      C2      N1
        1       1        N1      C2      C6      --> HERE
        1       2       O2*      C2*    C3*
        1       2       O3*      C3*    C4*

Do you think I made a mistake in this file ?

>
> >    N1	    NR    -0.28000     8
> >    H1     H       0.28000     8     --> HERE
> >    C6     C        0.38000     9
> >    O6	    O       -0.38000     9
> >    C5     C        0.00000    10
> >    N7	    NR     -0.36000    10
> >    C8     CR1    0.36000    10
> >   C2*    CH1    0.15000    11
> >   O2*    OA    -0.54800    11
> >
> > When I launch pdb2gmx, I have got a number of charges that is a float
> > instead of an integer (as expected). I found the origin of this error
> > looking at the generated itp file:
> >
> > 27    NR    1    GNP     N1      9      -0.28    14.0067   ; qtot -3.28
> > 28    H      1    GNP     H1     10   -0.15    1.008   ; qtot -3.43  -->
> > HERE 29    C      1    GNP     C6     11       0.38     12.011   ; qtot
> > -3.05 30    O      1    GNP     O6     11      -0.38    15.9994   ; qtot
> > -3.43 31    C      1    GNP     C5     12          0     12.011   ; qtot
> > -3.43 32    NR    1    GNP     N7     12      -0.36    14.0067   ; qtot
> > -3.79 33    CR1  1    GNP     C8     12       0.36     13.019   ; qtot
> > -3.43 34    CH1  1    GNP    C2*     13       0.15     13.019   ; qtot
> > -3.28 35    OA    1    GNP    O2*     13     -0.548    15.9994   ; qtot
> > -3.828
> >
> > First of all, the charge beared by the hydrogen H1 has been modified
> > (from 0.28000 to -15.0). Moreover, the group this atom belonged to has
> > been modified too (from 8 to 9)!
> >
> > Does anybody one have an idea ?
> >
> > Thanks in advance,
> > Mickael
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