Dear all,
I am experiencing a problem to convert the angle potential in a table.xvg
I have a polymer chain composed by 7 beads with two beadstypes A and B. The
polymer sequence is: A1-B1-B2-B3-B4-B5-A2. I have 2 bondtypes (AB and BB)
and two angletypes (ABB and BBB).
I obtained the dist.tgt. When I try to run the IBI it works for the bonds
but not for the angles. Because I supposed I was doing something wrong I
tried the hexane and propane tutorials to see if something was wrong with
my angles or my settings.xml and I am not able to obtained the tabulated
potential for angle neither for them.
This is the error I get:
ERROR:
#
# do_external: subscript
#
# /home/software/votca/share/votca/scripts/inverse/table_to_xvg.pl --max
1000000 --type angle ABB-angle.pot.shift.YkwA2 table_a0.xvg #
# (from tags convert_potential xvg) failed
#
# For details see the logfile inverse.logTHIS IS the DETAILS FROM THE inverse.log or_all: run 'do_external convert_potential gromacs $(csg_get_interaction_property name).pot.cur $(csg_get_interaction_property inverse.gromacs.table)' for interaction named 'ABB-angle' Running subscript 'potential_to_gromacs.sh ABB-angle.pot.cur table_a0.xvg' (from tags convert_potential gromacs) dir /home/software/votca/share/votca/scripts/inverse Convert ABB-angle.pot.cur to table_a0.xvg Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p' Running critical command 'mktemp ABB-angle.pot.scale.XXXXX' Running subscript 'table_linearop.pl --on-x ABB-angle.pot.cur ABB-angle.pot.scale.dHEeQ 57.2957795 0' (from tags table linearop) dir /home/software/votca/share/votca/scripts/inverse table_linearop.pl: ABB-angle.pot.cur to ABB-angle.pot.scale.dHEeQ with x' = 57.2957795*x + 0 Running critical command 'mktemp ABB-angle.pot.smooth.XXXXX' Running critical command 'csg_resample --in ABB-angle.pot.scale.dHEeQ --out ABB-angle.pot.smooth.bZWVq --grid 0:0.0286479:180' Running critical command 'mktemp ABB-angle.pot.extrapol.XXXXX' Running subscript 'potential_extrapolate.sh --type angle ABB-angle.pot.smooth.bZWVq ABB-angle.pot.extrapol.3ThKw' (from tags potential extrapolate) dir /home/software/votca/share/votca/scripts/inverse Extrapolate ABB-angle.pot.smooth.bZWVq to ABB-angle.pot.extrapol.3ThKw Running subscript 'table_extrapolate.pl --function linear --avgpoints 3 --region leftright ABB-angle.pot.smooth.bZWVq ABB-angle.pot.extrapol.3ThKw' (from tags table extrapolate) dir /home/software/votca/share/votca/scripts/inverse table_extrapolate.pl: extrapolating the left using linear with gradient -8.60697674418617 table_extrapolate.pl: extrapolating the right using linear with gradient -0.0167414651162821 Running critical command 'mktemp ABB-angle.pot.interpol.XXXXX' Running critical command 'csg_resample --in ABB-angle.pot.extrapol.3ThKw --out ABB-angle.pot.interpol.j2iBK --grid 0:0.0005:180 --comment Created on Thu Dec 18 16:38:36 EST 2014 by fstanzio@silicon called from potential_to_gromacs.sh, version 1.3-dev hgid: 4fce95a62b88 settings file: /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml working directory: /home/Documents/bigger_box/reaction/ibi_cou_user/step_001 Comments from /home/Documents/bigger_box/reaction/ibi_cou_user/step_001/ABB-angle.pot.cur:\nCreated on Thu Dec 18 16:38:30 EST 2014 by fstanzio@silicon called from prepare_generic_single.sh, version 1.3-dev hgid: 4fce95a62b88 settings file: /home/Documents/bigger_box/reaction/ibi_cou_user/settings.xml working directory: /home/Documents/bigger_box/reaction/ibi_cou_user/step_000' Running critical command 'mktemp ABB-angle.pot.shift.XXXXX' Running subscript 'potential_shift.pl --type angle ABB-angle.pot.interpol.j2iBK ABB-angle.pot.shift.YkwA2' (from tags potential shift) dir /home/software/votca/share/votca/scripts/inverse Running subscript 'table_to_xvg.pl --max 1000000 --type angle ABB-angle.pot.shift.YkwA2 table_a0.xvg' (from tags convert_potential xvg) dir /home/software/votca/share/votca/scripts/inverse *Illegal division by zero at /home/fstanzio/software/votca/share/votca/scripts/inverse/table_to_xvg.pl line 96.* Checking the xxx.pot.shift file I have "o" on the last 5 values, I tried to resample, to change the --grid to 179.5 (last value with "i") but nothing is working.. I have the version 1.3-dev. I am sending you in addition the ABB-angle.dist.tgt and the settings.xml files. Can you please help me to understand what is the problem and why I am not able to have a table_angle? Thank you, Francesca -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
ABB-angle.dist.tgt
Description: Binary data
settings.xml
Description: XML document
