The error message means that for some reason the safe_malloc() routine
in ptraj was asked to allocate a negative number of bytes of memory,
which shouldn't happen. I am able to run a similar set of commands on
a system I have with no problems. If possible could you attach the
relevant topology and coordinate files so I can reproduce the bug?
Also, have you run the test cases?
-Dan
PS - I noticed that you are referencing cryst.pdb but not using it in
the rms command (via rms reference instead of rms first) - is this
intentional?
On Tue, May 25, 2010 at 11:33 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> I have installed AmberTools 1.4 and the bugfixes. Everything works fine
> in ptraj except the rms function. This is my input file (rms.in) for an
> 81-residue protein:
>
>
>
> !#/bin/csh
>
> ptraj file.prmtop << EOF
>
> trajin fileprod.mdcrd
>
> reference cryst.pdb
>
> rms first mass out out.rms :1-81.CA time 1.0
>
> EOF
>
>
>
> When I run the script to calculate the rms values vs. time I get the
> following error message:
>
>
>
> ERROR in safe_malloc: Error in alloc of -8 bytes
>
>
>
> Can someone tell me what this error message means and how to correct it?
>
>
>
> Thanks!
>
>
>
> John
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 13:00:26 PDT
