VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 17 2017 - 07:14:29 CST

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.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.