AMBER Archive (2006)

Subject: Re: AMBER: Problem with setbox command...

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Mar 31 2006 - 06:34:33 CST

> > 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)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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