[gmx-users] Backmapping from MARTINI to AA in GROMACS 5.1.1: initram.sh error

SRINIVAS MUSHNOORI scm177 at scarletmail.rutgers.edu
Tue Dec 20 17:12:48 CET 2016

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

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 ...
... /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

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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