FLOR MARTINI wrote:
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.
PRODRG topologies are for use with Gromos force fields, so it will not work for
OPLS (many users have tried, and they are very disappointed). I do not know
what this business about editing .atp files is for - you shouldn't modify them
unless you are modifying the entire force field. Do you mean the .rtp files?
You can make modifications to it to define new residues so that pdb2gmx will
recognize them, but the .atp files generally remain unchanged.
Also important to note is that PRODRG topologies, taken at face value, are often
unsatisfactory, requiring manual modification, and validation, as always.
-Justin
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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--
========================================
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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