Adrien Delmont wrote:
The molecule I use is a simple hydrocarbon ( n-heptane ) and I think
that I should add something like dihedral, bond, angle parameters after
I search the literature. I found some information about that. I think I
will add parameters into the related force fields .itp file. Is it true
? And then I will create a box of 100 molecules without any error.
Most (if not all) of the parameters you will need will already be present in the
force field. No modification of any of these files should be necessary. If you
want to use pdb2gmx to create your topology, you need to create an .rtp entry.
For a simple alkane (especially with a UA representation), it should be trivial
to write the topology by hand with a text editor and a thorough understanding of
Chapter 5.
Alternate ideas:
1. Use PRODRG to generate a rough topology. Verify its contents before
proceeding, make any modifications you need, and validate the resulting topology.
2. Don't use Gromos96. AFAIK, none of the Gromos variants deal very well with
hydrocarbon chains. OPLS might be better, but I think there are some
limitations there, too.
-Justin
--- On *Wed, 3/11/09, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] get a box of 100 molecules
To: [email protected], "Discussion list for GROMACS users"
<[email protected]>
Date: Wednesday, March 11, 2009, 9:11 PM
Adrien Delmont wrote:
> I just want to add missing parameters for my molecule in order to get
...gro and top files for example GROMOS96 43a2 force field . How can I add
missing parameters ? I didn't find any information about this procedure.
I'm waiting for your help.
>
You'll have to define what you mean by "parameters" - is this
some new small molecule that has not been parameterized under this force field?
Are you starting from scratch? If so, this is not a trivial problem for a
beginner. Read here:
http://wiki.gromacs.org/index.php/Parameterization
If you have adequate parameters for most of your molecule and are missing
something like a dihedral, etc. then read the primary literature and derive
it
yourself. This process is also complicated, but is probably less work than
coming up with parameters for a brand new molecule.
-Justin
> Thanks in advance
>
>
> --- On *Wed, 3/11/09, Mark Abraham /<[email protected]>/*
wrote:
>
> From: Mark Abraham <[email protected]>
> Subject: Re: [gmx-users] get a box of 100 molecules
> To: "Discussion list for GROMACS users"
<[email protected]>
> Date: Wednesday, March 11, 2009, 4:58 PM
>
> Adrien Delmont wrote:
> > > >
------------------------------------------------------------------------
> > *From:* Adrien Delmont <[email protected]>
> > *To:* [email protected]
> > *Sent:* Wednesday, March 11, 2009 6:09:53 PM
> > *Subject:* Re: [gmx-users] get a box of 100 molecules
> > > I didn't get gro and top files with any force field
in Gromacs. I
> basicly want to use oplsaa and GROMOS96 43a2 force field (improved
alkane
> dihedrals) . I think I should add all the parameters but how can I
add my
> parametes both into oplsaa and GROMOS96 43a2 force field ?
>
> You can't just mix force fields. See
> http://wiki.gromacs.org/index.php/force_field
>
> Mark
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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
========================================
--
========================================
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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