Error with CoMD in VMD re autopsf

[rakeshr10]

Hi I get this error when I prepare my system

Unable to load file 'init.pdb' using file type 'pdb'.
Unable to load file 'init.pdb' using file type 'pdb'.
while executing
"mol new init.pdb"
(procedure "::comd::Prepare_system" line 81)
invoked from within
"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)

[jamesmkrieger]

I remember coming across this error before but I think it is now fixed. Please could you try using the latest version from github and see if you still get this error.

Thanks

[rakeshr10]

Hi I tried with both the latest VMD and coMD downloaded from github on coMD tutorial files. Still get the tk error.

ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
while executing
"segment $segid {
pdb $segfile

  # We alias the C-terminal OXT atoms to OT2 so that psfgen has to guess one atom less.
  # Otherwise psf..."
(procedure "psfsegments" line 37)
invoked from within

"psfsegments $logfileout"
(procedure "psfmain" line 93)
invoked from within
"psfmain"
(procedure "::autopsf::autopsf" line 123)
invoked from within
"::autopsf::autopsf -mol top -top {/home/rakesh/WORK/Projects/3-IntDynamics/5-GroELBench/NMA/comd/top_all36_prot.rtf /home/rakesh/WORK/Projects/3-IntDy..."
("eval" body line 1)
invoked from within
"eval ::autopsf::autopsf $args"
(procedure "autopsf" line 1)
invoked from within
"autopsf -mol top -top $::comd::topo_file -prefix pro"
(procedure "::comd::Prepare_system" line 87)
invoked from within
"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)

[jamesmkrieger]

Ok thanks. I’ll look into it and get back to you.

[jamesmkrieger]

Your new error is because the latest VMD has a problem with autopsf that makes it not compatible with CoMD. Please try VMD 1.9.2 or 1.9.3 instead.

I've also made some fixes to CoMD, which fixed some problems I had. Can you see if they fix your problems too please.

[jamesmkrieger]

Any luck with different VMD and CoMD versions?