[gmx-users] Using backward.py with Gromacs 5.x?

Peter Kroon p.c.kroon at rug.nl
Mon Jan 23 09:44:55 CET 2017

Hi Srinivas,

You're probably better off asking this on the Martini forum
(cgmartini.nl). What I would suggest for now (as a quick fix) is to
define bash aliases for grompp and mdrun, and have them point to gmx
grompp and gmx mdrun respectively. There might be more subtle effects as
well though. You have been warned.


On 22-01-17 20:12, SRINIVAS MUSHNOORI wrote:
> Dear GROMACS users,
> I'm attempting to backmap from a MARTINI CG representation to a CHARMM AA
> representation for my biomolecular system.
> The command I am using is:
> **./initram.sh -f FNF150-40out.gro -o charmm_FNF150-40.gro -to charmm36 -p
> FNF150-40.top**
> And the output I get is:
> **Checking dependencies:backward.py ...
> /md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.000000/backward.pygrompp ...
> Missing dependency: grompp**
> Now doing a bit of googling seemed to shed some light on the issue: GROMACS
> 5.x domes not seem to use a separate executable called "grompp" or even
> "mdrun" for that matter. Instead it simply uses one executable called gmx.
> Changing the dependency to the path of my gmx executable inside initram.sh
> and then attempting to run it gives me the following error:
> **Checking dependencies:backward.py ...
> /md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.000000/backward.py/usr/local/gromacs/bin/gmx
> <http://backward.py/usr/local/gromacs/bin/gmx>
> ... /usr/local/gromacs/bin/gmxTraceback (most recent call last):  File
> "/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.000000/backward.py", line
> 644, in <module>    struc =
> Structure(options["-f"].value,strict=options["-strict"].value)  File
> "/md1/scm177/Desktop/FF-FNF/FNF150-40-70/unit.000000/backward.py", line
> 411, in __init__    crsp.append(crsp[-1])IndexError: list index out of
> range*
> *
> I am unsure how to go about running the script. Any assistance on the
> matter will be immensely helpful.
> Thank you!
> Sincerely yours,
> Srinivas Mushnoori

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