Thank you Hai, Ross and Jason.
I am caught in this maze of force fields for IDPs. Since past 2 years I
have used ff14SB successfully to simulate IDPs and characterise a-turn and
PP-II structures in the ennsemble. More recently I got carried away with
literature which suggest use of ff03w and ff03ws with tip4p-2005 resulting
in balance of extended versus compact structure. Some research groups
further went ahead benchmarking various force fields including CHARMM22*
for IDPs (J. Chem. Theory Comput., 2015, 11 (11), pp 5513–5524) as well as
modifying gpu pmemd code around the LJ distances (Biochemistry, 2016, 55
(12), pp 1784–1800) however I believe they all ended up validating force
fields on different sets of peptides.
The chemical shift data on the peptide of my interest indicates presence of
CH-pi interactions and I couldn't quantify such interactions in my
simulations performed using force fields for IDPs. I am not sure whether it
is a sampling issue or a force field issue. Others have simulated identical
peptide using opls indicating presence of beta structure (Our NMR results
are not indicative of beta sheet). I am not sure if my question makes
sense, I am interested in knowing whether researchers have tried to
interpret CH-pi interactions in proteins using atomistic simulations. If
so, are force fields capable of looking at these sort of interactions? I
thought maybe CHARMM22* can do the job and hence my question above on using
CHARMM22* in amber.
On 7 April 2016 at 11:05, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Apr 6, 2016 at 8:37 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> > Dear List,
> >
> > Recently literature indicates preference for using CHARMM22* force field
> > (its ability to produce NMR observable) for simulations of intrinsically
> > disordered proteins. This force field is either available in gromacs or
> > ACEMD package.
> >
> > I am interested in simulating an IDP peptide with CHARMM22* force field
> and
> > advanced sampling techniques in AMBER. The use of pmemd.cuda will further
> > scale the simulations very well. However, AMBER does not support any
> > switching or shifting method for LJ interactions.
> >
> > I read paper on CHARMM-GUI where a hard-truncation method is used for
> > simulations of membrane in AMBER using CHARMM36 force field. Can I use a
> > similar protocol in AMBER to simulate IDP (without membrane) or I have to
> > consider some other parameters while using CHARMM22* force field in
> AMBER?
> >
>
> As I understand it, the force shifting method is required to reproduce
> reference CHARMM results for a couple kinds of lipids. Other types of
> systems display less sensitivity to the force switch vs. hard cutoff for
> Lennard-Jones interactions.
>
> At the end of the day, though, the "reference" results for the CHARMM 22
> force field is defined through the protocol employed to optimize the
> parameters. If using the force switch leads to results demonstrably
> different than *not* using the force switch, the not using the force switch
> is objectively wrong. This is the stance of every single force field
> developer in existence: if you use a different potential energy function
> than they did, *and you get different answers*, then you are not using the
> same force field. Very simple.
>
> One of the key points from the recent CHARMM-GUI paper was to lay out the
> suggested set of parameters to use with Amber to run the CHARMM force
> field. Which happens to be the standard 8 A hard cutoff for
> Lennard-Jones. I suggest using those until you can make use of the force
> switch in Amber 16.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Wed Apr 06 2016 - 19:00:04 PDT
