AMBER Archive (2006)

Subject: AMBER: error GRID command in ptraj

From: Andres Palencia (
Date: Thu Oct 26 2006 - 12:39:19 CDT

Hi everybody,

I am trying to calculate hydration density with the ptraj command grid
around the residue 51 of my system( complex protein-ligand). The
crystallographic water at the binding site were mainteined, and the
system was solvated with TIP3P waters prior to MD simulations. The
simulation was stopped at some point, so I restarted the system with the
last frame (it is the reason because I have got 2 files for mdcrc) The
input file for ptraj is as follow:

trajin ../ md1.crd
trajin ../ md2.crd
center : 51 mass origin
image origin familiar
rms first out rms_grid_51_wat : 51
grid grid_51_wat.xplor 100 0.25 100 0.25 100 0.25 : WAT

The coordinates from prmtop are read succesfully, although I have this
message "detected PBC angle in prmtop that in not 90. Asumming this box
is a truncated octahedron, angle is 109,471221" The machine starts to
process but suddenly I have got the error:

PTRAJ: center : 51 mass origin
*** glibc detected *** free() : invalid pointer : 0x0054a880 ***

Does anybody know what could be the problem?

Thanks in advance,

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