[gmx-users] (no subject)

[Luciane Vieira de Mello]

hi Anton,

I have already solved the ligand problem adding the
atom masses to ffgmx topology.
But, I confess I got a bit confused with ffgmx and gromacs forcefield
differences.
Things were going well, till I added ions to the system(to neutralize it).

genion -np 14 -s topol.tpr -o ion.pdb

grompp -f em.mdp -c ion.pdb -p topol_withGAD.top

and I got:
Cleaning up temporary file gromppNftfv9
Fatal error: No such moleculetype Na

no idea why, since I added:
#include "ions.itp"
to the topol.top file

What I did was to create a local Na.itp (copying it from ions.itp), and
grompp could find it.
However, it says:
Fatal error: Atoms in the .top are not numbered consecutively from 1

I cannot undersand why. I checked if everything is in the same
order as ion.pdb, and it is. If I delete all the Na from ion.pdb, grompp
runs fine. As soon as I add a single one, I get the message above.



any idea?

many thanks
Luciane


+-------------------------------------------------------------------------+
|                  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          |
+-------------------------------------------------------------------------+



On Thu, 6 Feb 2003, Daan Virtual wrote:

>
> Hi Lu
>
> That sounds like perhaps you are using the wrong force field with the
> PRODRG topologies. I think it is ffgmx that you should use, there is
> also a tutorial for doing this kind of thing on the PRODRG website.
>
> good luck
>
> Daan
>
> On Thu, 6 Feb 2003, Luciane Vieira de Mello wrote:
>
> >
> > Hi Daan,
> >
> > Hope  you are fine.
> >
> > Not sure if you saw my mail to gromacs list about Gromos and Gromacs
> > forcefields. The problem is I need to use ffG43a1 with SEP, TPO and PTR,
> > since there is a phosphoserine in the protein.
> > However, I made the ligand topology using PRODRG. I was trying to use the
> > gromacs topology output, and getting problems like, missing mass for the
> > ligand:
> > WARNING 5 [file "topol_withGAD.top", line 31434]:
> >   atom C2 (Res GAD-512) has mass 0
> >
> > Not sure how to add the masses to the topology file for gromacs.
> >
> > Then, I have decided to use the gromos topology file generated by PRODRG,
> > but I got the following message:
> >
> > topology... Generated 182 of the 1128 non-bonded parameter combinations
> > WARNING 1 [file "GAD_gromos.itp", line 1]:
> >   Too few parameters on line (source file toppush.c, line 867) WARNING 2
> > [file "GAD_gromos.itp", line 2]:
> >   Too few parameters on line (source file toppush.c, line 867)
> > Cleaning up temporary file gromppMhkZk3
> > Fatal error: Invalid dihedral type 4
> >
> > Have you got any idea how to solve this problem?
> >
> > thanks in advance
> > Luci
> >
> > +-------------------------------------------------------------------------+
> > |                  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
>
>