[gmx-users] pdb files
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 12 18:36:39 CET 2009
oguz gurbulak wrote:
> Will I write two .rtp files for two different molecules ? or Will I
> write one rtp file that includes all parameters of these two molecules
> ? And how can I use the rtp file when creating the input files ( .gro
> and .top ) ?
>
Read the manual, section 5.6.1.
-Justin
> Thanks in advance
>
>
> --- On *Thu, 3/12/09, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] pdb files
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thursday, March 12, 2009, 12:11 PM
>
>
>
> oguz gurbulak wrote:
> > Dear Justin,
> >
> > Can I get a itp file tempate for OPLS-AA according to your
> suggestions below and editing the itp file for my molecule. Is it
> possible to do this ? Or is there an alternative way apart from
> manually writing the itp file for OPLS-AA ?
> >
>
> You're stuck either writing an .rtp entry for use with pdb2gmx, or
> writing the .itp yourself.
>
> -Justin
>
> > Thanks in advance
> >
> >
> >
> > <<You will not want to create a topology from these files,
> because pdb2gmx would create a huge mess of files to deal with (a
> different topology for each chain). What you want is to do is to
> create .itp files for each individual molecule type in your system.
> This will probably have to be done by hand if you want to use
> OPLS-AA. Depending on the complexity of your molecule, you may be
> able to use an .rtp entry, but I would suggest processing a single
> molecule of this type with pdb2gmx to create a .top for that
> molecule (which can be converted to a .itp for later use).<<
> >
> >
> >
> > --- On *Sat, 3/7/09, Justin A. Lemkul /<jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] pdb files
> > To: gurbulakoguz at yahoo.com
> </mc/compose?to=gurbulakoguz at yahoo.com>, "Discussion list for
> GROMACS users"
> > <gmx-users at gromacs.org </mc/compose?to=gmx-users at gromacs.org>>
> > Date: Saturday, March 7, 2009, 9:28 AM
> >
> >
> >
> > oguz gurbulak wrote:
> > > > Dear All,
> > >
> > > > I want to use packmol pdb files that includes one
> or two
> > different types of molecules. And I seached Gromacs manuals,
> > tutorials and mail archives in order to have enough information
> > about using packmol pdb files in Gromacs. But I couldn't find any
> > information. So Could you please give me the information
> about this
> > ? How can I use a packmol pdb file for oplsaa and gromacs
> > united-atom force field in generating .gro and .top files for md
> > simulations?
> > >
> > >
> > You will not want to create a topology from these files, because
> > pdb2gmx would create a huge mess of files to deal with (a
> different
> > topology for each chain). What you want is to do is to
> create .itp
> > files for each individual molecule type in your system. This
> will
> > probably have to be done by hand if you want to use OPLS-AA.
> Depending on the complexity of your molecule, you may be able to use
> > an .rtp entry, but I would suggest processing a single
> molecule of
> > this type with pdb2gmx to create a .top for that molecule
> (which can
> > be converted to a .itp for later use).
> >
> > Do not use the "Gromacs force field" (ffgmx); it is
> deprecated and
> > should not be used for new simulations. Use a newer Gromos96
> > variant. You can get Gromos96-compatible topologies from the
> PRODRG
> > 2.5 server, but be warned that the charges and charge groups
> > assigned by PRODRG are often inconsistent and unsatisfactory,
> > requiring manual alteration and validation.
> >
> > Summary:
> > 1. Create .itp files for each molecule type individually.
> > 2. Construct a .top yourself, which would be as simple as:
> >
> > #include "ffoplsaa.itp"
> >
> > #include "molecule_A.itp"
> > #include "molecule_B.itp"
> >
> > #include "spc.itp"
> > #include "ions.itp"
> >
> > [ system ]
> > packmol system
> >
> > [ molecules ]
> > Molecule_A N
> > Molecule_B N
> > SOL N
> > (then whatever ions you need, if any)
> >
> > -Justin
> >
> > >
> > > Sincerely
> > >
> > > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> > >
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> > -- ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > 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
> Graduate Research Assistant
> 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
Graduate Research Assistant
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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