Re: trifluoroethanol (TFE) solvent

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Sep 10 2008 - 07:41:39 CDT

Hi Roman,

I had run simulations of peptides in TFE-water mixtures, using Alex's
force field, and have several long trajectories (> 200 ns total), but they
are of not much use to me now. You are welcome to take a look at them if
you want.

-Himanshu

----------------------------
Himanshu Khandelia, PhD,
Research Assistant Professor (Postdoc),
MEMPHYS, Center for BioMembrane Physics: www.memphys.sdu.dk
University of Southern Denmark (SDU)
Campusvej 55, Odense M 5230, Denmark
Phone: +45 6550 3510, +45 2398 7972
Fax: +45 6550 4048
email: hkhandel_at_memphys.sdu.dk, hkhandelia_at_gmail.com
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------

On Tue, 9 Sep 2008, Roman Petrenko wrote:

> thanks, at least i have the starting point.
>
> so, has anyone ran simulations of any protein solvated TFE?
>
> the first two comments in one of the files from MacKerell's website
> are very interesting :)
>
> Resi TFE 0.0 ! trifluoroethanol, not tested
> Group ! charges are not correct.
> Atom o1 oh1 -0.60
> Atom ho1 H 0.42
> Atom h11 HA2 0.09
> Atom h12 HA2 0.09
> Atom c1 CT2x 0.08
> Atom f21 f3 -0.14
> Atom f22 f3 -0.14
> Atom f23 f3 -0.14
> Atom c2 cf3 0.34
>
> Bond c1 h11 c1 h12 c1 o1 o1 ho1
> Bond c1 c2 c2 f21 c2 f22 c2 f23
>
> IC HO1 O1 C1 C2 0.0000 0.00 180.00 0.00 0.0000
> IC C2 O1 *C1 H11 0.0000 0.00 120.00 0.00 0.0000
> IC H11 O1 *C1 H12 0.0000 0.00 -120.00 0.00 0.0000
> IC O1 C1 C2 F21 0.0000 0.00 180.00 0.00 0.0000
> IC F21 C1 *C2 F22 0.0000 0.00 120.00 0.00 0.0000
> IC F21 C1 *C2 F23 0.0000 0.00 -120.00 0.00 0.0000
> patc firs none last none
>
>
>
>
>
> On Tue, Sep 9, 2008 at 9:39 PM, Christopher Gillespie
> <gillescche_at_gmail.com> wrote:
> > MacKerell has it here
> >
> > http://mackerell.umaryland.edu/CHARMM_ff_params.html
> >
> > Chris
> >
> >
> > On Sep 9, 2008, at 8:30 PM, Roman Petrenko wrote:
> >
> >> Dear namd community,
> >> does anyone have topology file for TFE (trifluoroethanol) solvent?
> >>
> >> --
> >> Roman Petrenko.
> >> Physics Department
> >> University of Cincinnati
> >>
> >
> >
>
>
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati
>
>

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