[gmx-users] pdb files

[Justin A. Lemkul]

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

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