[gmx-users] Regarding parameters of octane box in ffamber99sb - ildn

[Justin A. Lemkul]

YUVRAJ UBOVEJA wrote:
> Hello all
> 
> I have to create an octane box for studying effect of solvent 
> hydrophobicity on enzyme activation.
> Anyone using octane parameterized file in amber?
> Please suggest me how to parameterize it or is there any tutorial for it.
> As i am a beginner, so plz explain in steps.
> 

There is no substitute for reading the primary literature for your desired force 
field, and any previous publications upon which it is based.  These papers 
should tell you the proper methods for geometry optimization, charge 
calculations, etc.  Then, when you have a more thorough understanding of what 
approach you should take, you can post a more specific question about how to 
accomplish this task.

Parameterization is often not a task well-suited to beginners.  This should not 
discourage you from attempting your task, but please realize that the process of 
producing quality results is a long one, even for someone well-versed in exactly 
what is necessary.  Proper derivation of parameters can take weeks, months, or 
years, depending on how complicated the process is.  Take some time to learn how 
to use Gromacs for simple applications, understand the manual, understand your 
force field, then set out about your project.

Also, in the future, please do not include the entire digest when you post.  It 
confuses the archive.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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