Re: AMBER: Problem with setbox command...

From: Ilyas Yildirim <>
Date: Fri, 31 Mar 2006 07:34:33 -0500 (EST)

> > PS: I was thinking to copy/paste the box info of the first inpcrd_01
> >
> > 38.6491104 38.6491104 38.6491104 109.4712190 109.4712190 109.4712190
> >
> > to the second inpcrd_02.
> This is worth a try (i.e. it should work, but test carefully!). Another
> option is use just the solute for the second case, and use trial and error
> with distance parameter in solvateoct to get the desired number of water
> molecules.

Dear Dave,

I have done 2 simulation, using the following combinations:

1. inpcrd_01 and prmtop_01
2. inpcrd_01 and prmtop_02

They gave exactly the same output files. After this simulation, I have
replaced the last line of inpcrd_02 with the last line of inpcrd_01. I
have used 'ambpdb' to create the corresponding .pdb files; namely 01.pdb
which is created using inpcrd_01/prmtop_01, and 02.pdb, which is created
using prmtop_02/inpcrd_02_mod (inpcrd_02_mod is the modified version of
inpcrd_02). I checked out both these .pdb files in VMD, and the rmsd value
is 0.0008.

My conclusion: Changing only the last line of the inpcrd_02 with the last
line of inpcrd_01 should solve this 'setbox' problem. I did not do any
long simulation, because if prmtop files are not responsible of this
problem (which is the case after doing the above 2 simulations), that
means that only changing the last line of inpcrd file, which stores the
cell box info in it, is responsible of this problem.

Thanks for your suggestions. Best,

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 02 2006 - 06:10:15 PDT
Custom Search