VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 11 2011 - 09:22:22 CST

On Tue, Jan 11, 2011 at 5:09 AM, Michela Candotti
<michela.candotti_at_irbbarcelona.org> wrote:
> 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?

michela,

the error message is likely just a symptom of some other error elsewhere.

it is impossible, however, to give further help without having detailed
information and data to exactly reproduce this.

axel.

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

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.