You can automate this process if you have a large dataset and also directly convert to pdbqt format for autodock using this command: for file in *.sdf; do obminimize -o pdbqt -ff MMFF94 -n 1000 -h "$file" > "${file%.sdf}-minimized.pdbqt"; done
Thanks for the video; quite helpful. But as I have multiple ligand files in sdf format, I have downloaded each file separately so how to perform energy minimisation and convert these files into pdbqt format. Using windows.
Great video. But what about energy minimizing multiple ligand files....I have 886 files with each filename lig1.sdf, lig2.sdf....till lig886.sdf. However, when I am running your script with input filename as lig*.sdf it is giving me error "obminimize: cannot read input file!". Please help me resolve this issue!!
Sure i am working on it, currently i don't have that ubuntu system. So that i have to install Ubuntu in a new system. I will definitely do those videos. Thank you for waiting 😊
You can automate this process if you have a large dataset and also directly convert to pdbqt format for autodock using this command:
for file in *.sdf; do obminimize -o pdbqt -ff MMFF94 -n 1000 -h "$file" > "${file%.sdf}-minimized.pdbqt"; done
Thanks for the video; quite helpful. But as I have multiple ligand files in sdf format, I have downloaded each file separately so how to perform energy minimisation and convert these files into pdbqt format. Using windows.
Thanks for your video. I have a question. How to minimize the energy for many ligands at the same time?
Yeah soon I will post it on future videos
Great video. But what about energy minimizing multiple ligand files....I have 886 files with each filename lig1.sdf, lig2.sdf....till lig886.sdf. However, when I am running your script with input filename as lig*.sdf it is giving me error "obminimize: cannot read input file!". Please help me resolve this issue!!
One option is you shall combine all the sdf files into one then do the ligand minimization. Try this
sir can we minimize more than one molecules because i have to do for 3000 molecules and its very time consuming. And all the files are in mol format
yes can do that. I will post in next video. Stay tuned 👍
@@pymolbiomolecules Ok sir thank you
@@pymolbiomolecules Please do that, it will save a lot of time
Why I get can't open parameter file
Hello sir then how convert this file into actual structure
please help me with this problem : "could not find Van der Waals parameter for 1-37(IDX)
Thanks. Iam sorry because i want from you to post part 4 from series Molecular dynmic simaluation.
Sure i am working on it, currently i don't have that ubuntu system. So that i have to install Ubuntu in a new system. I will definitely do those videos. Thank you for waiting 😊
Ok. But don't late. Please 😊
Yeah sure, i have uploaded the part 4. Thanks for tuned in 👍
Thank you very much