Re: [AMBER] error regarding periodic prmtop

From: Jio M <>
Date: Sun, 12 Dec 2010 23:24:26 -0800 (PST)

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

 imin = 5, ntb = 0,
 gbsa = 2, surften = 1,
 igb = 1, ntwx = 1,
 cut = 1000

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)


--- On Mon, 12/13/10, Jason Swails <> wrote:

From: Jason Swails <>
Subject: Re: [AMBER] error regarding periodic prmtop
To: "AMBER Mailing List" <>
Date: Monday, December 13, 2010, 6:19 AM


My comments are below:

On Sun, Dec 12, 2010 at 11:55 PM, Jio M <> 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

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

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,

> 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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Sun Dec 12 2010 - 23:30:02 PST
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