[gmx-users] reverse transformation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 16 19:14:49 CET 2012

Hi Francesca,

Can you post your complete workflow?



On Feb 16, 2012 7:04 PM, "francesca vitalini" <
francesca.vitalini11 at gmail.com> wrote:

Hi all!
I'm having some issues with the reverse transformation, so I decided
to start from a toy system, alias the 1UBQ present in the martini
tutorial. After running the ./martinize script., before any energy
minimization, I try to reverse the transformation and I encounter the
following error message.

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 started everything from the 1UBQ.pdb from which I have deleted the
water, with ./martinize.py I obtain a cg.top and a cg.gro.
using the GROMACS 3.3.1 version of pdb2gmx I get the aa.top

Trying to reconvert from cg to aa I obtain the message pasted before.
Any ideas?

Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120216/5db0f56c/attachment.html>

More information about the gromacs.org_gmx-users mailing list