[gmx-users] Gromacs for reverse transformation
shivangi nangia
shivangi.nangia at gmail.com
Fri May 23 22:51:29 CEST 2014
Hi Tsjerk,
Thanks so much for all the help.
I tried both 2.6.5 and 2.7 versions
both on running python on backward.py give the following error:
Traceback (most recent call last):
File "backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "backward.py", line 318, in __init__
self.atoms = [pdbAtom(i,strict) for i in lines if isPDBAtom(i) or
rest.append(i)]
TypeError: 'NoneType' object is not iterable
sxn
On Fri, May 23, 2014 at 3:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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 It means your python version is outdated.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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