VMD-L Mailing List

From: Michela Candotti (michela.candotti_at_irbbarcelona.org)
Date: Tue Jan 11 2011 - 04:09:14 CST

Dear VMD users,
I'm using NAMD energy plugin (1.2) to calculate energy between protein and
solvent, using different selections..
my script contains those lines:

namdenergy -sel $sel1 $sel2 -updatesel -vdw -elec -par par_opls_aa.inp
-ofile x1 -switch 11 -cutoff 13 -plot -exe path/to/namd2
namdenergy -sel $sel1 $sel3 -updatesel -vdw -elec -par par_opls_aa.inp
-ofile x2 -switch 11 -cutoff 13 -plot -exe path/to/namd2

The first namdenergy command is working correctly but at the end (after
the first output is written) I receive this error:

invalid command name "toplevel"

and thus vmd is force to exit and cannot go on with the second command
line..

Someone has an idea why my version of VMD (VMD for LINUXAMD64, version 1.8.7
and also 1.8.6) cannot recognise toplevel as a command? and maybe how can I
fix it?

Thanks,

Michela Candotti
Phd Student
Barcelona Supercomputing Center (BSC) / Institute for Research in
Biomedicine (IRB)
C/ Baldiri Reixac 10
08028 Barcelona, Spain.