[gmx-users] PEO and OPLS-AA FF in gmx

[Justin A. Lemkul]

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 /<jalemkul at vt.edu>/* escribió:
> 
> 
>     De: Justin A. Lemkul <jalemkul at vt.edu>
>     Asunto: Re: [gmx-users] PEO and OPLS-AA FF in gmx
>     Para: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     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

========================================