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

[SRINIVAS MUSHNOORI]

Thank you, Peter. I will post on the forum.

On Mon, Jan 23, 2017 at 3:44 AM, Peter Kroon <p.c.kroon at rug.nl> wrote:

> 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.
>
>
> Peter
>
>
> 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/backw
> ard.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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