Re: Namd-I: Implicit solvent problem

From: Giovanni Settanni (gs_at_mrc-lmb.cam.ac.uk)
Date: Thu Jun 30 2011 - 01:56:13 CDT

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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