[gmx-users] Chage modifications with pdb2gmx

[David van der Spoel]

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?
> 
>    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
> _______________________________________________
> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++