Re: Re: Namd-I: Implicit solvent problem

From: Matteo Rotter (matteo.rotter_at_uniud.it)
Date: Wed Jul 20 2011 - 16:06:29 CDT

Hi Enrico.
Thanks for the reply. I'm testing specifically this protein for its beaviour.
I know the lack of treatment of the hydrophobic part but the point
here is the different results for same implicit solvent model.
One: minimization+run in one .conf= unfolding.
Second: minimization (.conf) -> run (.conf) = stable.

Quoting Enrico Guarnera <enrico.guarnera_at_gmail.com>:

> Hi there,
>
> this happens because the GBIS model as implemented in NAMD 2.8 does not
> include an implicit treatment of the hydrophobic effect or the non-polar
> effects due to the solvent but only the electrostatics.
> It would really great if the NAMD team could consider to address this
> problem in a future version of the program (for example adding a SASA
> module...).
>
> Best,
> Enrico
>
> On Wed, Jul 20, 2011 at 12:04 PM, Matteo Rotter
> <matteo.rotter_at_uniud.it>wrote:
>
>> Dear All,
>>
>> I have tried to perform simulation of this Ankyrin protein.
>> I found some results that i would like to share with you. Please let me
>> know what you think about.
>>
>> 1st: as Ye Yang wrote, the protein seems really stable in explicit solvent
>> simulation.
>> 2nd: in implicit solvent(gb): if i perform minimization and run in the same
>> simulation (one .conf file) the protein rapidly unfolds in very few
>> picoseconds.
>> 3rd: in implicit solvent(gb): performing minimization and run with two
>> different runs of namd will not affect the stability of protein. Also using
>> same seed between 2nd and 3rd and inside 3rd between minimization and run.
>>
>> What do you think about?
>>
>> Regards,
>> Matteo.
>>
>> Quoting Giovanni Settanni <gs_at_mrc-lmb.cam.ac.uk>:
>>
>> Maybe you may try the protocol that we used in this paper
>>> http://www.ncbi.nlm.nih.gov/**pubmed/20371329>
>>> to pull other similar ankyrin proteins. we used EE1 and FACTS implicit
>>> solvent models that are available in charmm.
>>>
>>> On 06/30/2011 12:44 AM, Ye Yang wrote:
>>>
>>>> Also, if I use explicit solvent, this protein will be very stable at 400K
>>>> for 10 ns simulation, which is not experimentally true, and I
>>>> need a box of
>>>> ~60nm waterbox. Any suggestions which approach should I use?
>>>> Thanks
>>>>
>>>> Ye
>>>>
>>>> 2011/6/29 Ye Yang <
knightyangpku_at_gmail.com <mailto:knightyangpku_at_gmail.*
>>>> *com <knightyangpku_at_gmail.com>>>
>>>>
>>>> Hi, Frencesco and Gianluca:
>>>> Thanks for replying.
>>>> Yes, it is the repeat Ankyrin protein... So maybe it is no
>>>> good for using the implicit solvent?
>>>> The problem right now is that I would like to pull the
>>>> ankyrin protein at a certain temperature (300K), so I need to
>>>> equilibrating it first, as long as it is stable in room
>>>> temperature, it will be fine for me.
>>>> For my case, some of my friends did coarse grained
>>>> simulation in vacuum, yet they seem do not have any trouble in the
>>>> unexpected unfolding, I am not sure what is going on if I use
>>>> all-atom.
>>>> Thank you very much.
>>>> Ye
>>>>
>>>>
>>>> 2011/6/29 Gianluca Interlandi <gianluca_at_u.washington.edu
>>>> <mailto:gianluca_at_u.washington.**edu <gianluca_at_u.washington.edu>>>
>>>>
>>>> I suspect that E3_19 might not be stable with this type of
>>>> implicit solvent model (it doesn't contain a term to take the
>>>> non-polar solvation energy into accout). You should simulate
>>>> it in explicit water (or try one of the implicit solvent
>>>> models implemented in CHARMM, but I doubt it).
>>>>
>>>> If by E3_19 you mean the designed Ankyrin Repeat Protein, I
>>>> know people who tried different implicit solvent models a
>>>> while ago. None really worked. But I might be mistaken and by
>>>> no means I want to be discouraging.
>>>>
>>>> Gianluca
>>>>
>>>>
>>>> On Wed, 29 Jun 2011, Francesco Oteri wrote:
>>>>
>>>> Hi Ye,
>>>> maybe you are using a too small cut-off..Try with a value
>>>> greater than 30A
>>>>
>>>> Francesco
>>>>
>>>>
>>>> Il 29/06/2011 23:07, Ye Yang ha scritto:
>>>>
>>>> Dear Namd expert:
>>>> I am trying to use implicit solvent model to
>>>> simulate my protein E3_19, which is thermally stable
>>>> through experiment and full molecule simulation(above
>>>> 400K in simulation for over 10ns).
>>>> However, once I am using the imlicit solvent, it
>>>> even unfolds at 300K, which is really weird, could
>>>> anyone explain to me what is happening and how I can
>>>> solve this?
>>>> Also, what I am thinking is to increase the
>>>> damping factor, but what should I typically use?
>>>> Thank you very much.
>>>>
>>>> exclude scaled1-4
>>>> 1-4scaling 1.0
>>>> cutoff 18.
>>>> switching on
>>>> switchdist 12.
>>>> pairlistdist 22
>>>>
>>>>
>>>> langevin on ;# do langevin dynamics
>>>> langevinDamping 5 ;# damping coefficient
>>>> (gamma) of 5/ps
>>>> langevinTemp $temp
>>>> langevinHydrogen no ;# don't couple langevin
>>>> bath to hydrogens
>>>>
>>>>
>>>> if {1} {
>>>> GBIS on
>>>> solventDielectric 78.5
>>>> intrinsicRadiusOffset 0.09
>>>> ionConcentration 0.2
>>>> GBISDelta 1.0
>>>> GBISGamma 4.85
>>>> alphaCutoff 15
>>>> }
>>>>
>>>> No BC and No PME for my simulation
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------**-----------------------
>>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>> <mailto:gianluca_at_u.washington.**edu <gianluca_at_u.washington.edu>>
>>>> +1 (206) 685 4435
>>>>
>>>> http://artemide.bioeng.**washington.edu/>
>>>>
>>>> Postdoc at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> ------------------------------**-----------------------
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>> ------------------------------**------------------------------**----------
>> SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine
>>
>>
>>
>

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SEMEL (SErvizio di Messaging ELettronico) - CSIT -Universita' di Udine

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