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