How to do Energy minimization of proteins via CHIMERA||What is energy minimization??CHIMERA tutorial

Hello students
Enjoy this video tutorial about energy minimization via CHIMERA tool
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[@boorasanjit2013]

excellent video

[@maxars9510]

Hello! How to resolve this error: Element H (atom #0:1.A@H) is not currently supported [no GAFF type]?

[@dnadatadive]

give me the screenshot of the error and then may be i will be able to help

[@memoryabigal964]

When do we get a video on steepest decent steps. How do you calculate that part?

[@dnadatadive]

I will try to upload it 🔜

[@deneshrajs2705]

Sir, Can you explain how to examine a protein for missing loops and residues? and How to build the missing loops?

[@dnadatadive]

this is aseparate concept of loop refinement i guess this paper will help you. Have a look at it
www.nature.com/articles/s41598-018-32079-w

[@deneshrajs2705]

@@dnadatadive Is loop refinement necessary for docking and MD studies?

[@dnadatadive]

@@deneshrajs2705 without it also you can do your simulation but it is recommended to get better results and also if you want to publish your data then it is required

[@MohamedAsifSMSB]

homology modelling

[@AsadKhan-we7sx]

start the video from 9:06

[@hanstsahnang4533]

Hello dear sir is the default parameters of Chimera for protein minimisation sufficient for publication?

[@dnadatadive]

Yes it should be but alone chimera results won't result in a publication rather the complete study needs to be sufficiently revelant

[@hanstsahnang4533]

@@dnadatadive I'm try to perform virtual screening on my protein target and I want to minimize the protein structure while keeping the parameters on default. Default parameters for minimisation should be sufficient in this case?

[@dnadatadive]

@@hanstsahnang4533 The aim of this minimization is to find a stable protein confirmation for your protein molecule that you generated by different protein modeling tools. Yes the default parameters are sufficeint for your study

[@smani7954]

How to energy minimization 1000 compound at same time? Available any server

[@smani7954]

Tell me please

[@dnadatadive]

if you want to do 1000 molecules simaltenously then open separate windows of chimera and upload different molecules. but you need to have high computing power for 1000 molecules. However, I son't know any server that can do this kind of work

[@dnadatadive]

@@smani7954 already told you na