Hello,
I am having a problem, I cannot identify how to solve.
I am doing IBI of bonded interactions and so I get an error.
There must be smth wrong between cg-mapping.xml and topol.top files, but I
cannot spot what. I also get error of same type if I run
csg_dump as a check.
Thank you!
List of molecules:
--------------------------------------
WARNING: unknown molecule "DCG" with id 0 in topology
Reading frame 0 time 0.000 molecule will not be mapped to CG
representation
Check weather a mapping file for all molecule exists, was specified in --cg
separated by ; and the ident tag in xml-file matches the molecule name
--------------------------------------
Reading frame 50 time 10.000 an error occurred:
Topology does not have beads of type "C"
This was specified in type1 of interaction "C-C"
Callstack:
/share/apps/votca/share/votca/scripts/inverse/inverse.sh - linenumber 252
do_external - linenumber 170 in
/share/apps/votca/share/votca/scripts/inverse/functions_common.sh
/share/apps/votca/share/votca/scripts/inverse/update_ibi.sh -
linenumber 31
for_all - linenumber 17 (see 'csg_call --cat function for_all')
do_external - linenumber 18 (see 'csg_call --cat
function do_external')
/share/apps/votca/share/votca/scripts/inverse/calc_rdf_generic.sh -
linenumber 71
critical - linenumber 4 (see 'csg_call --cat
function critical')
die - linenumber 2 (see 'csg_call --cat
function die')
#########################################################################################################################################################################################
#
#
#
ERROR:
#
# critical: 'csg_stat --nt 8 --options /home/valentina/CG/GAS/settings.xml
--top topol.tpr --trj traj.xtc --begin 10 --first-frame 0 --cg
/home/valentina/CG/GAS/cg-mapping.xml' failed #
# For details see the logfile
/home/valentina/CG/GAS/inverse.log
#
#
#
#########################################################################################################################################################################################
die: (called from 7667) CSG_MASTER_PID is 7125
die: pids to kill: 0
On Friday, September 28, 2012 2:07:44 PM UTC+1, Valentina wrote:
>
> Hello!
>
> I am a little confused here.
>
> I have read somewhere that Votca 1.3 (? I thought latest version is 1.2.3)
> supports IBI for bonded - is this right?
>
> If so, how do I implement it? I have attatched my settings file (saved in
> .odt,but used as .xml on the machine). This doesn't seem to do more then
> fitting the nonbonded C-C potential. Am I missing something?
>
> Many thanks!
> Valentina
>
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