Perhaps you can do your parametrization. Enter to the prodrg page and you will
see!
The page is:
http://davapc1.bioch.dundee.ac.uk/prodrg/
and you will get your .gro and .top, and you don't need to use the pdb2gmx. If
you want to use it anyway, you need to edit the data base, but I think that the
manual is not very clear for this item.
I think that you should see the .atp they are in the
--/gromacs/share/top/ffGxx.atp where xx is the force field that you would use.
See your .pdb also and compare the atoms that there are not defined.
Cheers.
Flor
Dra.M.Florencia Martini
Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas
Cátedra de Química General e Inorgánica
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 2º (1113)
TE: 54 011 4964-8249 int 24
--- El vie 25-sep-09, Justin A. Lemkul <[email protected]> escribió:
De: Justin A. Lemkul <[email protected]>
Asunto: Re: [gmx-users] PEO and OPLS-AA FF in gmx
Para: "Discussion list for GROMACS users" <[email protected]>
Fecha: viernes, 25 de septiembre de 2009, 12:32 pm
lammps lammps wrote:
> Hi,
> I want to simulate a PEO chain in water using OPLs-AA FF in Gromacs.
> I have created a .PDB file using Material Studio, but I seems that the
>pdb2gmx can not dealt with it because of the error" Residue 'xx' not found in
>residue topology database"
> The question is how can I obtain the .top and .gro file in the framework of
> OPLS-AA FF. Any suggestion is appreciated.
>
You have to derive parameters for yourself:
http://www.gromacs.org/Documentation/How-tos/Parametrization
There are a few scripts in the User Contributions section that make efforts to
do this for you, but you still have to demonstrate that the parameters are
valid.
-Justin
> Thanks in advance.
>
> -- wende
>
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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