Hi Patrick, On 08/03/2011 03:47 PM, Patrick Kiley wrote: > 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? > yes, that is how things are supposed to be. The first path is the 'source code' including the scripts. When you compile and install it gets copied to the prefix dir, ~/votca in your case. You probably pulled a new version and did not install it using the build.sh script.
-Sebastian > 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.
