[gmx-developers] problem with the reverse transformation coarse grained to all atom

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 17 15:17:13 CET 2012

francesca vitalini wrote:
> Dear all,
> I'm trying to make a reverse transformation from cg to aa work, so I
> started from a toy system. Took the pdb and converted in topology, run
> the ./martinize.py script and obtained a cg.top cg.gro and cg.pdb.
> Unfortunately, when I try the reverse transformation I encunter the
> following error:
> Number of fg atoms 25
> Number of cg atoms 5
> Reading frames from gro file 'MODEL        1', -1 atoms.
> -------------------------------------------------------
> Program g_fg2cg, VERSION 3.3.1
> Source code file: smalloc.c, line: 113
> Fatal error:
> calloc for fr->x (nelem=-1, elsize=12, file confio.c, line 919)
> -------------------------------------------------------
> "I Need Love, Not Games" (Iggy Pop & Kate Pierson)
> : Cannot allocate memory
> Any idea what it means?

This is a memory allocation error.  Please realize that g_fg2cg is not an 
official Gromacs program and thus you may have better luck contacting the 
MARTINI group for troubleshooting.  Some of them may be on this list, but I 
don't know.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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