[MMTK] problems with molecular dynamics

michael.l.stoppelman.1 stoppeml@purdue.edu
Fri, 8 Nov 2002 03:41:46 -0500 (EST)


I seemed to have fixed this problem.

I am trying to write a  program that will build a peptide chain an amino
acid at a time. I am new to MMTK and was wondering if anyone could help me
out.

My first idea is to extend the PeptideChain class adding a addResidue
method.  After every addition to the PeptideChain I want to minimize the
energy over that chain. I attempted to do this with only two residues and
I got a bus error.

But first, I wanted to see if any of this would even work:

from MMTK import *
from MMTK.Minimization import SteepestDescentMinimizer
from MMTK.ForceFields import Amber94ForceField
from MMTK import Proteins
from MMTK import Biopolymers

# just gets the sequence of letters
residues = 'MVCA' # my protein sequence
universe = InfiniteUniverse(Amber94ForceField())
p = Proteins.PeptideChain(residues[0:2], model = 'no_hydrogens')
universe.addObject(p) # probably wrong
minimizer = SteepestDescentMinimizer(universe)
minimizer(steps = 10)

that code core dumps.

any ideas?

-Mike



On Thu, 7 Nov 2002, michael.l.stoppelman.1 wrote:

> Hey guys,
>
> I am seeing some interesting problems, MMTK is core dumping in a library.
>
> SunOS:
>
> $ python
> Python 2.1 (#1, May 22 2001, 11:19:26)
> [GCC 2.95.2 19991024 (release)] on sunos5
> Type "copyright", "credits" or "license" for more information.
> >>> from MMTK.Minimization import SteepestDescentMinimizer
>
> Segmentation fault (core dumped)
>
>
> Cygwin:
>
> $ python
> Python 2.2.1 (#1, Jun 25 2002, 10:55:46)
> [GCC 2.95.3-5 (cygwin special)] on cygwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from MMTK.Minimization import SteepestDescentMinimizer
> Segmentation fault (core dumped)
>
>
> Here is an truss on SunOS:
> ==== SNIP =====
> open("/home/champion/l/stoppeml/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_trajectory.so",
> O_RDONLY) = 5
> fstat(5, 0xFFBFC648)                            = 0
> open("/home/champion/l/stoppeml/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_trajectory.so",
> O_RDONLY) = 6
> fstat(6, 0xFFBFBF84)                            = 0
> mmap(0x00000000, 8192, PROT_READ|PROT_EXEC, MAP_PRIVATE, 6, 0) =
> 0xFF330000
> mmap(0x00000000, 98304, PROT_READ|PROT_EXEC, MAP_PRIVATE, 6, 0) =
> 0xFEED0000
> mmap(0xFEEE6000, 4516, PROT_READ|PROT_WRITE|PROT_EXEC,
> MAP_PRIVATE|MAP_FIXED, 6, 24576) = 0xFEEE6000
> munmap(0xFEED8000, 57344)                       = 0
> resolvepath("/home/champion/l/stoppeml/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_trajectory.so",
> "/home/champion/l/stoppeml/cs590b/lib/python2.1/site-packages/MMTK/sunos5/MMTK_trajectory.so",
> 1023) = 91
> memcntl(0xFEED0000, 5884, MC_ADVISE, MADV_WILLNEED, 0, 0) = 0
> close(6)                                        = 0
> munmap(0xFF330000, 8192)                        = 0
>     Incurred fault #6, FLTBOUNDS  %pc = 0xFEED62A0
>       siginfo: SIGSEGV SEGV_MAPERR addr=0x00000004
>     Received signal #11, SIGSEGV [default]
>       siginfo: SIGSEGV SEGV_MAPERR addr=0x00000004
>
> Any ideas?
>
> -Mike
>
>
>
>
>
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