Re: Namd-I: Implicit solvent problem

From: Matteo Rotter (matteo.rotter_at_uniud.it)
Date: Wed Jul 20 2011 - 11:04:03 CDT

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>>
>>
>> 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>>
>>
>> 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>
>> +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.
>> -----------------------------------------------------
>>
>>
>>
>
>

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