[gmx-users] pdb files

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> 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.
> 

I'll add to this that there really isn't an ".itp template" - it's just a 
topology without the call for the force field, and without [ system ] and [ 
molecules ] directives

-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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>>
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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

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