[gmx-users] pdb files

[oguz gurbulak]

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 ?

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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