[gmx-users] PRODRG - .itp file

[Daan Virtual]

Hi Lu

If I try

O     O
|     |
C-C-O-P=O
" |   |
O C-O O

it seems to come out OK with all non-C atoms carrying partial charges?
The double torsion angle is required (I guess) to take into account some
of the more bulky orbitals on P. This was also used in GROMOS87 and that's
essentially the same as the ffgmx forcefield in GMX.

cheers

Daan

On Tue, 17 Dec 2002, Luciane Vieira de Mello wrote:

>
> Dear all,
>
> I 've been using the excellent PRODRG server with success recently, but
> I'm having some unexpected problems this time.
>
> My ligand is 2-phosphoglycerate.  The only change I made to the
> PRODRG-derived parameters (the .itp file) was to make the three chemically
> equivalent atoms the same in terms of charge etc. The problem is that
> after energy minimization with these parameters, the phosphate group
> becomes distorted.  The distortion is quite marked - see attached snapshot
> and pdb file.  I've tried various things but I always get the distortion.
> The only thing in the itp file which looks strange is the double entry for
> one of the dihedrals
>
>    6   5   2   1   1   0.0    1.0 3   0.0    1.0 3 ; DI     C2  O1P    P
> O4P
>    6   5   2   1   1   0.0    3.1 2   0.0    3.1 2 ; DI     C2  O1P    P
> O4P
>
> However, when I delete either one the distorion is much worse!
>
>
> Can anybody help?
>
> Thanks in advance
>
>
>
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
>
>
>
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O