VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jan 17 2017 - 14:07:19 CST

To elaborate a bit further, Tcl evaluates the inside of strings for
commands inside of brackets, since those are evaluated first. This
causes a parser error, since ... isn't a command. The way this is
handled elsewhere is to selectively escape brackets, so changing the
offending line like so:

vmdcon -info "J.V. Vermaas et al., TopoGromacs: \[...\]"

or simply commenting it out will also fix the error. Thanks again for
pointing out the problem!

-Josh

On 01/17/2017 07:01 AM, Axel Kohlmeyer wrote:
> On Tue, Jan 17, 2017 at 4:30 AM, Igor Ariz <iarizex_at_gwdg.de> wrote:
>> Hi all,
>>
>> I'm trying to build a gromacs topology file using topotools. Since I want to
>> use the topology file to
>> run simulations, I am using the syntax specified in the topotools
>> documentation providing also the charmm
>> parameter files.
>>
>> Nonetheless, the following command seems to fail:
>>
>>> Main< 70 % topo writegmxtop structure.top [list paramfile1.prm
>>> paramfile2.prm]
>> Info) ======================
>> Info) Please cite the following publication:
>> invalid command name "..."
>>
>> Noteworthy, the previous command without the "[list paramfile1.prm
>> paramfile2.prm]" works properly,
>> generating a topology file that cannot be used for simulations.
> thanks for the report. this is a bug that crept into topotools just
> before the release of the latest VMD version.
>
> if you locate the file topogromacs.tcl (should be in
> $VMDHOME/plugins/noarch/tcl/topotools1.7/ )
> and apply a change like the following, it should work again.
>
> diff --git a/topogromacs.tcl b/topogromacs.tcl
> index ddfd2d8..e8fdb5d 100644
> --- a/topogromacs.tcl
> +++ b/topogromacs.tcl
> @@ -48,7 +48,7 @@ proc ::TopoTools::writegmxtop {filename mol sel
> {flags none}} {
> if {$gmxciteme} {
> vmdcon -info "======================"
> vmdcon -info "Please cite the following publication:"
> - vmdcon -info "J.V. Vermaas et al., TopoGromacs: [...]"
> + vmdcon -info "J.V. Vermaas et al., TopoGromacs: Automated
> Topology Conversion ..."
> vmdcon -info "http://dx.doi.org/10.1021/acs.jcim.6b00103"
> vmdcon -info "======================\n"
> set gmxciteme 0
>
>
>
> axel.
>
>> Thanks in advance.
>>
>> Igor.
>>
>
>