AMBER Archive (2003)

Subject: Re: Sander box error and thanks on previous mdin error

From: kxg2248_at_njit.edu
Date: Fri Jan 03 2003 - 11:37:05 CST

At 10:40 AM 1/3/03, you wrote:
>On Thu, Jan 02, 2003, kxg2248_at_njit.edu wrote:
> >
> > Here is the error message I get after the restart:
>
> > getting new box info from bottom of inpcrd
> > | peek_ewald_inpcrd: Box info not found in inpcrd
>
>This is correct: your restart file does not have any box information in it,
>and it should be there. You can check yourself: the box information is
>the final line of the file, with 6 numbers (x,y,z and three angles, which
>are probably 90.)
>
>But with only 24 atoms in your system, do you really want this to be
>periodic? Amber is not designed to handle crystals with very small unit
>cells, or otherwise extremely small periodic systems. What is the chemical
>system you are simulating? How did you set it up in LEaP, i.e. did you
>use the setBox or solvateBox commands?
There are 54 atoms in the system - 30 of them are in the "belly" and kept
still. It is a DNA/small molecule system. One nucleotide pair and a small
molecule. I used the example in the manual for set up using antechamber
and leap. I didn't setBox as it wasn't mentioned in the example. The
inpcrd file is the prmcrd file created by antechamber using my pdb
containing all 3 molecules.

One thing different than in the sander example in the manual was that I
read that belly can only be used when ntb=0, so I changed it from ntb=2 in
the example. As may be obvious, I am new to using AMBER, and I am more
used to using GUI molecular modeling programs that have a lot of defaults
available. I see that I had ntb=1 in my mdin noted in my last posting, I
have to look into why I changed it. My understanding is that I can't run a
periodic boundary condition with belly atoms.

Thanks,
K. Gilbert