[gmx-users] hexafluoroisopropanol

[Justin Lemkul]

On 10/4/12 1:34 AM, Nur Syafiqah Abdul Ghani wrote:
> Hi Guys,
>
> Need your help urgently.
> I already read a lot of paper about molecular dynamics simulation
> which relate work as mine.The main point is to create the mix solvent.
> The co-solvent is hexafluoroisopropanol and a lot of researcher cited
> the journal name "1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular
> dynamics simulations" by Fioroni.
>
> So my question,is the molecule already have a pdb structure?Have
> anyone dealing with this compound?

Constructing a coordinate file for a small organic molecule is rather simple 
with any number of tools.

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

> Because im currently lost due to my HFIP pdb is wrong and the atom
> type of F is not recognized and the force field i used is OPLSAA but
> right now i think i need to change it to the
> GROMOS96..Your advise are highly appreciate..
>

You should not presume that one force field is inherently better than another 
for an arbitrary molecule that is not already parameterized.  One could produce 
reliable parameters for any force field, provided care is taken to derive and 
evaluate them properly.

There seem to be two threads with nearly identical problems.  Perhaps you can 
cross-reference some information with the other active thread.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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