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prody / coMD

This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization
http://prody.csb.pitt.edu/comd/
MIT License
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Error with CoMD in VMD re autopsf #51

Open rakeshr10 opened 6 years ago

rakeshr10 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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

jamesmkrieger commented 5 years ago

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 commented 5 years ago

Any luck with different VMD and CoMD versions?