Nothing stands out as wrong. If it's working that's probably a good sign.
On Mon, Dec 13, 2010 at 2:24 AM, Jio M <jiomm.yahoo.com> wrote:
> Thanks Jason,
>
> I followed suggestion its working now. I did following
>
> 1) used prmtop without water or periodic (new prmtop created)
>
> 2) used restart file after stripping water, nobox
>
> 3)from trajectory also strpped water, nobox
>
> 4) input file being
>
> &cntrl
> imin = 5, ntb = 0,
> gbsa = 2, surften = 1,
> igb = 1, ntwx = 1,
> cut = 1000
> &end
>
> please let me know if I am wrong (initially trajene error like was coming I
> searched in archive and as suggested by Carlos I used ntwx=1)
>
> thanks;
> JIomm
>
> --- On Mon, 12/13/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] error regarding periodic prmtop
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, December 13, 2010, 6:19 AM
>
> Hello,
>
> My comments are below:
>
> On Sun, Dec 12, 2010 at 11:55 PM, Jio M <jiomm.yahoo.com> wrote:
>
> > Dear AMBER users,
> >
> > It is discussed in archive regarding SASA calculations over a trajectory
> > but I am ending with error if I use this input (similar to, as discussed
> in
> > archive):
> >
> > &cntrl
> >
> >
> > imin = 5,
> >
> >
> > gbsa=2,
> >
> >
> > surften=1
> >
> >
> > cut=1000, igb=1
> >
> > error is ::
> > Error: ifbox=2 in prmtop but angles are not correct
> >
>
> This means that the prmtop file, when built with leap, you most likely used
> the "solvateoct" command to produce a solvated system. The analysis above
> seems to suggest that you're trying to do some kind of MM/PBSA analysis
> (extracting the surface areas as your subject suggests). In this type of
> analysis, you will typically have no waters, and no periodic boundary
> conditions.
>
> GBSA, surften, and igb are all incompatible with periodic systems, which
> your prmtop is clearly set up for. How did you create your prmtop? Does
> it
> have waters present? If it does have waters present, you should create a
> new prmtop without waters (and therefore without periodic boundary
> conditions), and use ptraj to strip the waters from your trajectory, in
> order to use the above input file. Also don't forget to set ntb=0 in your
> input file, since that is the flag for periodic boundary conditions, and by
> default it is set to 1. However, note that for your system, just setting
> ntb=0 will most likely NOT work, since your prmtop is set up for periodic
> systems.
>
> Also, a prmtop created by using the "stripwater" command in rdparm and then
> dumped back out again will typically NOT work for a simulation, and is only
> useful for visualization (in my experience).
>
> Hope this helps,
> Jason
>
> >
> >
> > This is due to prmtop is periodic file so as suggested by David Case in
> > archive not to set igb=1 and also setting igb =0, its not accepting. So
> what
> > value I should use to remove this error. I used upto igb=5 but same error
> is
> > coming.
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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AMBER mailing list
AMBER.ambermd.org
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Received on Mon Dec 13 2010 - 09:30:03 PST
