Re: [AMBER] Implicit Solvent simulation - membrane proteins

From: Ray Luo <rluo.uci.edu>
Date: Mon, 11 Apr 2016 11:21:47 -0700

Hi Balaji,

Looks like you are trying to use the PB module for your minimization.
However, you can't use PB in such jobs for membrane proteins.

Only single point calculations such as those in mmpbsa are currently
supported. We are not planning to add force interpolation for membrane
systems in the near future.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Apr 11, 2016 at 10:51 AM, Balaji Selvam <bselvam01.gmail.com> wrote:
> Dear AMBER Users,
>
> I am trying to simulate a membrane protein using implicit solvent model.
>
> Using amber14 manual, I prepared the minimization file (min.in) however i
> failed in this step.
>
> The prmtop and inpcrd files are generated using tleap and i didn't solvate
> the box and the files does not contain peroidic boundary information.
>
> However, in min.in file I used options membraneopt=1, peroidic boundary
> conditions (bcopt=10) as there is a option to simulate with boundary
> conditions (as mentioned in amber14 manual page 77).
>
> The min.in file input commands are shown below
>
> minimize structure
>
>  &cntrl
>
>  /
>
>  &pb
>
>  /
>
>  imin=1,
>
>  maxcyc=1000,
>
>  membraneopt=1,
>
>  solvopt=1,
>
>  bcopt=10,
>
>  eneopt=1,
>
>  sasopt=2,
>
>  epsmemb=1.0,
>
>  cut=999.0,
>
>  rgbmax=999.0,
>
>  igb=8,
>
>  saltcon=0.15,
>
>  phiout=1,
>
>  phiform=1,
>
>  intdiel=1.0,
>
>  extdiel=78.5,
>
>  ntpr=100,
>
>  ntx=100,
>
>  ntr=1,
>
>  restraintmask'.CA,C,O,N',
>
>  restraint_wt=5.0
>
> /
>
>
> However, running the sander command shows error as " no box info found in
> inpcrd file".
>
> Kindly advice how to include box information for implicit solvent models in
> prmtop and inpcrd files.
>
> Also, I would like to know is there any amber tutorial for implicit
> membrane protein simulation.
>
> Thank You,
> Balaji
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Received on Mon Apr 11 2016 - 11:30:03 PDT