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
>
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Received on Thu Sep 30 2010 - 05:00:05 PDT
