AMBER Archive (2008)

Subject: RE: AMBER: Minimization in Octahedric Box

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 06 2008 - 12:22:39 CDT

Hi Carlo,

> x = sequence { NARG ASP HIE SER TYR GLN GLU CGLU }
> solvateoct x TIP3PBOX 8.0
> addions x Na+ 0
> saveamberparm x mog_101-108_ext_watoct.top mog_101-108_ext_watoct.crd
> savepdb x mog_101-108_ext_watoct.pdb
> quit

> Unfortunately at the end of the minimization run, I realized that the box
> was deformed and in particular 6 satellite clouds of water appeared around
> the main cloud surrounding the peptide (see attached files).

Well that's just plain weird!!!

Here's what I tried:

> tleap
source leaprc.ff99SB
x = sequence { NARG ASP HIE SER TYR GLN GLU CGLU }
solvateoct x TIP3PBOX 8.0
addions x Na+ 0
saveamberparm x prmtop inpcrd
savepdb x initial.pdb
quit

Loading the initial.pdb or the prmtop+inpcrd into VMD looks good.

I then created minimize.in

Minimization
 &cntrl
  imin = 1,
  maxcyc = 5000,
  ncyc = 2500,
  ntb = 1,
  ntr = 1,
  cut = 12.0,
 /
Keep protein fixed
500.0
RES 1 8
END
END

And then ran amber9 with:

mpirun -np 2 /usr/local/amber9/exe/sander.MPI -O -i minimize.in -o
minimize.out -p prmtop -c inpcrd -r minimize.rst -ref inpcrd

Loading the prmtop and minimize.rst files into VMD still look great. Also:

ambpdb -p prmtop < minimize.rst > minimize_ambpdb.pdb

Also produces a pdb that looks fine.

The resulting files are attached. Hence I can't work out how you got what
you did - very weird. This could well be some strange bug. Have you run all
the amber test cases? Do they all pass? Also did you run this in serial or
parallel? If it is in parallel could you try re-running it in serial please.

Also if you post exactly what you did - I.e. how you created the pdb's etc
as well as posting your output etc it may help to track things down.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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