Dear Daniel,
Sorry for the delayed reply and thanks for your prompt reply. I tried as
you suggested. Such a jump in memory usage happens only when I do the
molsurf calculation with entire complex (1- 505) and with 202-407. The
calculation was successful with 1-201 and 408-505. It also worked fine when
I did calculation with :1-202,408-505 together. Its quiet surprising what
is going wrong with the rest of the protein.
Many thanks
Anu
On Thu, Oct 29, 2015 at 6:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This is a strange error, especially since 'molsurf' shouldn't need
> anywhere near that much memory for any reasonable # of atoms - for
> example, for 34,686 atoms the memory requirement is about 168 MB.
>
> My initial advice would be to run each 'molsurf' command separately to
> see if it is one of them in particular that is causing the issue.
> Also, you don't need to 'autoimage' prior to 'molsurf' (imaging has no
> effect on the 'molsurf' calculation).
>
> -Dan
>
> On Wed, Oct 28, 2015 at 6:48 AM, anu chandra <anu80125.gmail.com> wrote:
> > Hello,
> >
> > I am trying to do SASA calculation with molsurf module in CPPTRAJ in
> > AmberTools 15. Unfortunately, the program got hanged with a sudden jump
> in
> > memory usage from 1.5 GB to 30 GB of RAM and it showed the following
> > message on the terminal,
> >
> > edge: 21883 v1: 22169 v2: 20158
> > edge: 21892 v1: 20165 v2: 17260
> > edge: 21894 v1: 22187 v2: 22054
> > edge: 21896 v1: 22043 v2: 22188
> > edge: 0 v1: 3 v2: 0
> > edge: 3588 v1: 3951 v2: 3954
> > edge: 21902 v1: 22197 v2: 20128
> > edge: 21904 v1: 22191 v2: 22197
> > edge: 21906 v1: 20132 v2: 22194
> > terminate called after throwing an instance of 'std::bad_alloc'
> > what(): std::bad_alloc
> >
> >
> >
> > Below, please find the cpptraj input commands.
> >
> >
> > **********************************************************
> > trajin md1.crd
> >
> > autoimage
> >
> >
> > molsurf d1 :1-505 out d1_SASA.dat probe 1.3
> >
> > molsurf d2 :1-201 out d2_SASA.dat probe 1.3
> >
> > molsurf d3 :202-407 out d3_SASA.dat probe 1.3
> >
> > molsurf d4 :408-505 out d4_SASA.dat probe 1.3
> > ***************************************************************
> >
> > Please help me to figure out what went wrong with the calculation here.
> >
> > Many thanks
> > Anu
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 11 2015 - 05:30:06 PST
