Yea, I realized after I sent the reply that you were in fact overwriting the
same variable, which should free up the memory (but it wasn't). I've never
actually had any problem with reduce properly adding hydrogen atoms for
me...
There are a couple options open: does sleap work? It uses the same
templates, and it is more recent. Perhaps sleap does not show the same
memory leak issues.
As a final resort, you can quit tleap after each pdb is created and fire it
up again for the next molecule. That is almost certain to free up the
memory.
Hope this helps,
Jason
On Thu, Sep 30, 2010 at 7:48 AM, Martin Brieg <martin.brieg.kit.edu> wrote:
> Hello,
>
> i tried using pymol, reduce and openbabel for this. The Problem with these
> tools is that they dont add all hydrogens. They skip those that are clashed
> with other parts of the protein. tleap does add all hydrogens in all cases
> and
> it also has a good scheme of naming/numbering the newly added atoms in a
> consitent way, which saves me alot of time and headaches afterwards.
>
> i tried the "remove pdb" after every pdb file i saved e.g.
>
> pdb = loadPdb file1.pdb
> savePdb pdb file1.pdb
> remove pdb
>
> however that didnt resolve the problem. i also tried "clearVariables pdb",
> but
> that didnt help either.
>
> Best,
> Martin
>
> > On second thought, "remove" might do this. In any case, I still think
> > reduce is the way to go.
> >
> > On Wed, Sep 29, 2010 at 9:44 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> > > Hi Martin,
> > >
> > > I don't know if it's necessarily a memory leak -- there's no reason to
> me
> > > why the memory should be getting freed in the first place based on the
> > > commands you gave (in fact, I don't know if there even is a 'delete'
> > > command). My suggestion would actually be to use the "reduce" program
> to
> > > add hydrogens to the PDB files rather than using leap. Reduce is
> described
> > > in the ambertools manual.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > >
> > > On Wed, Sep 29, 2010 at 9:34 AM, Martin Brieg <martin.brieg.kit.edu
> >wrote:
> > >
> > >> Hello everyone,
> > >>
> > >> I am using tLeap to add hydrogens to heavy atom trajectories of MD
> > >> simulations
> > >> and large decoy sets. However i have noticed a very fast increase of
> > >> memory
> > >> usage of tleap when loading and saving alot of pdb files:
> > >>
> > >> the script for tleap looks like the following:
> > >>
> > >> source leaprc.ff03.r1
> > >> pdb = loadPdb file1.pdb
> > >> savePdb pdb file1.pdb
> > >> pdb = loadPdb file2.pdb
> > >> savePdb pdb file2.pdb
> > >> pdb = loadPdb file3.pdb
> > >> savePdb pdb file3.pdb
> > >> ...
> > >>
> > >> The memory usage increases to 1 GB in about a minute or two and goes
> even
> > >> further. Is this really a memory leak? Or is leap writing to some
> hidden
> > >> variables that are not apparent from the input script and just need to
> be
> > >> cleaned from time to time? If so, how do i do this?
> > >>
> > >> Regards
> > >> Martin
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 30 2010 - 06:30:03 PDT
