Hi,
I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipids so I wonder is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?
1) Kukol, A., 2009. Lipid models for united-atom mol
Here is another paper related to the secondary structure propensity
of different force field.
Are current Molecular Dynamics FFs too helical? Best et al:
BiophysJ-2008
doi:10.1529/biophysj.108.132696
Note that these papers do not report the unstability of helices in
proteins!
On Jan 22,
Thank you!!!
The evidence presented in this paper is stunning. It also stresses the
importance of using the electrostatics treatment that was originally used
for development of a particular force field, e.g. reaction field in case of
G96 - the popular PME in connection with G53a6 results in even st
Hello,
I'm very happy that so many people contributed to the subject of the
(in)validity of using G53a6 for alpha helical proteins.
Thank you for the links.
I know now that I certainly should use a different force field from the
GROMOS96 family, which maintains alpha helices where they should be an
Hi,
Well, we have compared the G53a5/6 force field with the 43a2 one and
found consistently larger radii of gyration and higher RMSDs,
suggesting decreased stability. There's a thorough account of it in my
thesis
(http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/04emb_c4.
It is documented. Have a look at this one:
Dirk Matthes and Bert L. de Groot. Secondary structure propensities in
peptide folding simulations: A systematic comparison of molecular
mechanics interaction schemes. Biophys. J. 97:599-608 (2009)
Erik
XAvier Periole skrev:
The instability of
The instability of helices with the G53a6 force field is definitely real
and unfortunately not documented. Some people are working on it ...
I would advise to be very carefull in interpreting results with this FF.
XAvier.
On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
Krzysztof Mlyna
Krzysztof Mlynarczyk wrote:
2010/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
Krzysztof Mlynarczyk wrote:
2. If not, is there any way to derive the proper parameters for
the force field of my choice using the lipid parameters from
Peter Tieleman's website or
2010/1/21 Justin A. Lemkul
>
>
> Krzysztof Mlynarczyk wrote:
>
> 2. If not, is there any way to derive the proper parameters for the force
>> field of my choice using the lipid parameters from Peter Tieleman's website
>> or e.g. the parameters published by Andreas Kukol for G53a6?
>>
>>
> I don'
lto:
> gmx-users-boun...@gromacs.org]
> > On Behalf Of Justin A. Lemkul
> > Sent: 21 January 2010 01:36
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields
> >
> >
> >
> > Justin A. Le
ussion list for GROMACS users
> Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields
>
>
>
> Justin A. Lemkul wrote:
> >
> >
> > Krzysztof Mlynarczyk wrote:
> >> Hello,
> >>
> >> On Peter Tieleman's website we can find to
Justin A. Lemkul wrote:
Krzysztof Mlynarczyk wrote:
Hello,
On Peter Tieleman's website we can find topologies for various popular
lipids. However those seem to be valid for the deprecated GROMOS87
force field. The g96_lipids.itp file is still unavailable. I'd like to
run a simulation of
Krzysztof Mlynarczyk wrote:
Hello,
On Peter Tieleman's website we can find topologies for various popular
lipids. However those seem to be valid for the deprecated GROMOS87 force
field. The g96_lipids.itp file is still unavailable. I'd like to run a
simulation of 7TM protein embedded into P
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