[gmx-users] Gromacs for reverse transformation

Fri May 23 21:50:20 CEST 2014

Hi sxn,

Now that's rather unfortunate! Python 3.x has distinct differences in
syntax. If you can (also) install 2.7. Otherwise, maybe it's time I adapt
the program for python 3... :p

Cheers,

Tsjerk
On May 23, 2014 9:25 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
wrote:

> Hi Tsjerk,
>
> Thanks so much for the reply.
>
> I updated to python version 3.3.2
>
> and  I tried to run the backward.py using python3 backward.py
>
> I get the following error:
>
>  File "backward.py", line 351
>
>     try:
>
>        ^
>
> TabError: inconsistent use of tabs and spaces in indentation
>
>
> May be its a minor thing to fix but I am not familiar with Python.
>
> Thanks,
> sxn
>
>
> On Fri, May 23, 2014 at 2:09 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi sxn,
> >
> > It means your python version is outdated. The function 'all' was
> introduced
> > in version 2.5. Better upgrade to 2.7. If you really can't I can maybe
> > write a workaround.
> >
> > Cheers,
> >
> > Tsjerk
> > On May 23, 2014 5:31 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
> > wrote:
> >
> > > Dear Tsjerk,
> > >
> > > My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and
> > > ions.
> > >
> > > I realize that for all-atom the topology file should not contain
> details
> > > for water and ions.
> > >
> > > As a test while trying to understand and get familiarized with
> backward.
> > >
> > > As of now I am trying to convert CG peptide only to all-atom.
> > >
> > > I am using the following command:
> > >
> > > ./initram.sh -f protein.gro -p topol.top -from martini -po
> backmapped.top
> > > -to gromos54a7
> > >
> > > (I obtained the topol.top file for the peptide by using: pdb2gmx -f
> > > peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water)
> > >
> > > The script is giving me the following error:
> > >
> > > Traceback (most recent call last):
> > >
> > >   File "/shared/maylab/shivi/fhv/inverse_cg/try1/backward.py", line
> 644,
> > in
> > > ?
> > >
> > >     struc =
> > Structure(options["-f"].value,strict=options["-strict"].value)
> > >
> > >   File "/shared/maylab/shivi/fhv/inverse_cg/try1/backward.py", line
> 388,
> > in
> > > __init__
> > >
> > >     if not all(chain):
> > >
> > > NameError: global name 'all' is not defined
> > >
> > >
> > > Could you please help.
> > >
> > >
> > > Thanks,
> > >
> > > sxn
> > >
> > >
> > > On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury <iitdckc at gmail.com
> > > >wrote:
> > >
> > > > Dear Tsjerk,
> > > >
> > > > Thanks.
> > > >
> > > > I will definitely get in touch.
> > > >
> > > > Chandan
> > > >
> > > >
> > > > On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar <
> tsjerkw at gmail.com
> > > > >wrote:
> > > >
> > > > > Hi Chandan,
> > > > >
> > > > > You may have to write a mapping file, as explained in one of the
> > > > tutorials
> > > > > in the supplementary information of the paper. If that poses
> > problems,
> > > > you
> > > > > can contact me. I may be interested in adding new mappings :)
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Tsjerk
> > > > > On May 22, 2014 6:42 PM, "Chandan Choudhury" <iitdckc at gmail.com>
> > > wrote:
> > > > >
> > > > > > Hi Tsjerk,
> > > > > > Do the scripts available in the backward.zip file
> > > > > >
> > > >
> > http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp
> > > > > > me to backmap a coarse-grained polymer?
> > > > > >
> > > > > > Chandan
> > > > > >
> > > > > >
> > > > > > On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar <
> > tsjerkw at gmail.com
> > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi sxn,
> > > > > > >
> > > > > > > I would argue that that method for reverse transformation is
> > > largely
> > > > > > > obsolete. Please have a look at
> > > > > > > http://www.cgmartini.nl/cgmartini/index.php/back
> > > > > > >
> > > > > > > Cheers,
> > > > > > >
> > > > > > > Tsjerk
> > > > > > >
> > > > > > >
> > > > > > > On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> > > > > > > <shivangi.nangia at gmail.com>wrote:
> > > > > > >
> > > > > > > > Hello,
> > > > > > > >
> > > > > > > > I want to do a reverse transformation of my system
> containing:
> > > > > > bi-layer,
> > > > > > > > protein and water.
> > > > > > > >
> > > > > > > > The Martini website (
> > > > > > > >
> > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation
> > > )
> > > > > says
> > > > > > > to
> > > > > > > > install gromacs version 3.3.1
> > > > > > > >
> > > > > > > > I am currently using 4.6.1 gromacs version.
> > > > > > > >
> > > > > > > > ques A: Is this version incapable of the transformation?
> > > > > > > >
> > > > > > > > Also, the martini website says to:
> > > > > > > >
> > > > > > > > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL
> > directory
> > > > > that
> > > > > > > > contains all necessary gromacs files for this exercise.*
> > > > > > > >
> > > > > > > > *2. Compile and/or source the modifi ed version of gromacs
> > > > (remember
> > > > > > this
> > > > > > > > tool is based upon gromacs version 3.3.1 and needs the
> > > > corresponding
> > > > > > > tricks
> > > > > > > > and threats to be compiled.)*
> > > > > > > >
> > > > > > > > *source
> /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> > > > > > > >
> > > > > > > >
> > > > > > > > ques B:On performing untar on rev_trans.tar.gz there is no
> > > > > > > MARTINITUTORIAL
> > > > > > > > directory
> > > > > > > > ques C: On performing untar on gmx_rev.tar.gz there is no bin
> > > > folder
> > > > > > > >
> > > > > > > > KIndly help.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > sxn
> > > > > > > > --
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> > > > > > >
> > > > > > > --
> > > > > > > Tsjerk A. Wassenaar, Ph.D.
> > > > > > > --
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> > > > > > --
> > > > > >
> > > > > > --
> > > > > > Chandan Kumar Choudhury
> > > > > > National Chemical Laboratory, Pune
> > > > > > India
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> > > > --
> > > >
> > > > --
> > > > Chandan Kumar Choudhury
> > > > National Chemical Laboratory, Pune
> > > > India
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