Hi sxn, It means your python version is outdated.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.nan...@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 <iitd...@gmail.com > >wrote: > > > Dear Tsjerk, > > > > Thanks. > > > > I will definitely get in touch. > > > > Chandan > > > > > > On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar <tsje...@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" <iitd...@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 <tsje...@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.nan...@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 > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore > > > > > > posting! > > > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor > > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Tsjerk A. Wassenaar, Ph.D. > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > -- > > > > Chandan Kumar Choudhury > > > > National Chemical Laboratory, Pune > > > > India > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > > > -- > > Chandan Kumar Choudhury > > National Chemical Laboratory, Pune > > India > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
