[gmx-users] pdb files

[oguz gurbulak]

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 )  ?

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>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] pdb files
>     To: gurbulakoguz at yahoo.com, "Discussion list for GROMACS users"
>     <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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