Couldn't be able to generate psfgen bash script while generating DruGUI system

prody / DruGUI

Druggability Suite

http://prody.csb.pitt.edu/drugui/

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Couldn't be able to generate psfgen bash script while generating DruGUI system #15

Open ThilibanManivarma opened 1 year ago

ThilibanManivarma commented 1 year ago

I did generate the drugui.pdb, drugui.psf ( files from DruGUI - preparation of system ) successfully but I could not be able to run psfgen script as I would like to add few ions to it. The system contain probes like Acetamide(ACAM), Acetate(ACET), Isopropanol(IPRO), [Isopropylamide(IPAM)] and I have all the required parameter files but still I can't generate the psfgen, I can clearly see that there's a problem while psfgen script reading "par_all27_prot_lipid_na.inp"

please find the log file I attached,

log_problemdruGUI.txt

jamesmkrieger commented 7 months ago

If you only have one parameter file for protein, lipid and nucleic acid, then it’s not surprising there’s a problem with ions because there’s another parameter file for water and ions.

Sorry about not replying in so long. I’m not working on drugui any more and just thought about checking it for no particular reason

jamesmkrieger commented 7 months ago

Sorry, I looked at your error more closely now and I think the problem is it’s trying to read a parameter file when it wants a topology one. Perhaps you selected the wrong files in the wrong boxes?

jamesmkrieger commented 1 month ago

Which vmd version are you using? I think psfgen changed between vmd versions and you should probably go back to vmd 1.9.2 to get it working