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