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akohlmey / topotools

VMD plugin for manipulating topology information
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Error "can't read "cmaptmp": no such variable" when trying to write gmx top #23

Open kpounot opened 1 year ago

kpounot commented 1 year ago

Hi everyone,

I am trying to generate gmx topologies for my protein, which so far worked great. But I got a bug recently that I could not solve thus far.

I have attached the files that generate the bug here (.psf, .pdb and the .prm file for cobalamin). You will see there are some bonds that should not be there (generated by psfgen) that I usually remove manually in the .top file.

I am using VMD v1.9.4a53 with topotools v1.8. The command I use is:

topo writegmxtop structure.top [list par_cobalamins.prm]

which results in the error:

 Info) Generating a real gromacs topology file: structure.top
    can't read "cmaptmp": no such variable

Interestingly, I do not get any error if I do not give an output file name, but I don't get a .top file neither:

topo writegmxtop [list par_cobalamins.prm]

Best, Kevin

topotools_bug.zip

kpounot commented 1 year ago

My bad, I just realized that I initially forgot the output file name and used: topo writegmxtop [list par_cobalamins.prm]

Such that the parameter file has been overwritten with the topology. The error was coming from me.

What about having the parameter list as a flag option to avoid this?