Hi,
1. igb8 is not optimized for membrane protein and I don't think amber has
good implicit solvent for this kind of simulation.
2. GB in AMBER does not support PBC.
In my opinion, you should use explicit water + GPU. But if you really
really want to come with implicit solvent, you can check CHARMM
(google: charmm membrane implicit solvent)
cheers.
Hai
On Mon, Apr 11, 2016 at 1:51 PM, 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 11 2016 - 11:00:04 PDT
