Hi Christoph, I figured it out. Running "find /home/patrick/ -name *potential*" indicates that there are actually two copies of the script on my machine: /home/patrick/votca/src/csg/share/scripts/inverse/ potential_to_gromacs.sh /home/patrick/votca/share/votca/scripts/inverse/ potential_to_gromacs.sh.
Is this how things are supposed to be? Anyway, I only knew about one of them, but when I checked the other one, it had the typo. After I changed it, everything worked perfectly. Thanks again! Patrick On Aug 3, 1:55 pm, Sebastian Fritsch <[email protected]> wrote: > Hi Patrick, > > I just checked with my installation of the latest version - it works. > Are you sure you are using the updated version of > votca/share/votca/scripts/inverse/potential_to_gromacs.sh? The faulty > version should contain > "tableend", the 2 e's being the typo. Did you maybe accidentally source > the wrong votca version? You can check using 'csg_call --show > convert_potential gromacs' which script it is actually calling. > > Hope it helps, > Sebastian > > > > > > > > > Hi Christoph, > > > Thanks for your reply. I visually inspected potential_to_gromacs.sh > > to make sure it's the most recent version, which it is. > > Unfortunately, the problem remains. Any other ideas? > > > Kind regards, > > Patrick > > > On Aug 3, 12:22 pm, Christoph Junghans <[email protected]> wrote: > > >> Hi Patrick, > > >> there was a small typo in potential_to_gromacs.sh, Victor fixed it a while > >> ago: > >> <http://code.google.com/p/votca/source/detail?r=89b4c1ab41a67acca31375...> > > >> Soupdatevotca, or change this two lines in your installation. > > >> Cheers, > > >> Christoph > > >> 2011/8/3 PatrickKiley<[email protected]>: > > >>> Dear all, > > >>> I would be greatful for any help provided, and apologies in advance if > >>> this is an obvious problem! I have recently had success converting > >>> bond potentials to gmx input (i.e "table_bx.xvg") using the command: > >>> csg_call --ia-type bonded --options tempfil.xml convert_potential > >>> gromacs my_pot.fitted table_b0.xvg > > >>> tempfil.xml > >>> <cg> > >>> <inverse> > >>> <gromacs> > >>> <pot_max>1000000</pot_max> > >>> <table_bins>.002</table_bins> > >>> <table_end>4</table_end> > >>> </gromacs> > >>> </inverse> > >>> </cg> > > >>> This works very well. Gromacs accepts the tabulated potentials and > >>> runs fine. > > >>> However, I am now trying to do the same for angle potentials similarly > >>> to what I found here: > >>>http://groups.google.com/group/votca/browse_thread/thread/3926812904d... > > >>> csg_call --ia-type angle --options tempfil.xml convert_potential > >>> gromacs my_pot.fitted table_a0.xvg > > >>> Unfortunately this fails with the output: > >>> wrong range format, use min:step:max > >>> ###################################################################################################################################################################################################################################################################################################################################################################################### > >>> # > >>> # > >>> # > >>> ERROR: > >>> # > >>> # critical: 'csg_resample --in BBA14-BBD15-BBA16.angle.dat.fitted -- > >>> out smooth_BBA14-BBD15-BBA16.7nKSd --grid 0:.002: --comment Created on > >>> Wed Aug 3 11:49:36 BST 2011 by patrick@pjk38 > >>> called from potential_to_gromacs.sh, version 1.2 > >>> settings file: /home/patrick/data/cg/rada/atomistic/map1/tempfil.xml > >>> working directory: /home/patrick/data/cg/rada/atomistic/map1' failed # > >>> # > >>> # > >>> ###################################################################################################################################################################################################################################################################################################################################################################################### > > >>> I can't figure out why this is happening. I can see that the range > >>> given in the error ("0:.002:") is definitely wrong because it is > >>> missing the final value, but how do I fix this, and why would it work > >>> for bonds but not angles? > > >>> Kind regards, > >>> Patrick > > >>> -- > >>> You received this message because you are subscribed to the Google Groups > >>> "votca" group. > >>> To post to this group, send email [email protected]. > >>> To unsubscribe from this group, send email > >>> [email protected]. > >>> For more options, visit this group > >>> athttp://groups.google.com/group/votca?hl=en. > > >> -- > >> Dr. Christoph JunghansVotcaCore Developer > > >> Web:http://www.votca.org -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
