Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra <>
Date: Mon, 3 Dec 2007 13:45:14 -0800 (PST)

Great! With

1st minimization protein_ligand_pop_box80x80
  imin=1, maxcyc=20, ntmin=2,
  cut=10, ntb=1, ntpr=1,
  ntr=1, restraintmask=":77-520, 521",

it completed the (small) task (third attempt, in parallel). It should not be
forgot that I had removed some severe clashes before the third attempt: the
first attempt would have probably killed even steepest descent (not tried,
though I could try on demand for maxcyc=20, ncyc=10). Now I'll try maxcyc=500,
otherwise as in the successful run.

Thanks a lot


--- "David A. Case" <> wrote:

> On Mon, Dec 03, 2007, Francesco Pietra wrote:
> > I removed all WAT residues at a distance <=1.5A from POPC residues from the
> > membrane already bearing a cavity. Then inserted the protein-complex and
> > built the TIP3P box with leap. Then run the minimization again. Starting
> > energy was 9 orders of magnitude less that previous run (which had crashed
> > because WAT 534 had clashes with POP 24) and gradient and energy decreased
> > by only 2 orders of magnitude. Again segmentation fault.
> Segmentation faults can be very difficult to diagnose, since there can be
> many
> causes. Ordinarily, sander would not segfault on minimization just because
> of bad overlaps.
> What I would do:
> 1. Try a serial minimzation to see if there is some weird parallelization
> problem. You are only trying to do a short minimization, so you should
> reduce
> your exposure to other problems.
> 2. Only do steepest descent minimization with a bad structure. Conjugate
> gradient minimization (which by defaults starts after 10 steps,) can take
> very
> large trial steps, which might somehow be violating implicit assumptions
> about
> periodicity that leads to memory corruption (just guessing here, but avoiding
> conjugate gradients until you have a better structure is definitely a good
> idea.)
> 3. If that fails, you will probably have to remove the initial bad contacts
> and see if that helps.
> ...dac
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Received on Wed Dec 05 2007 - 06:07:20 PST
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