18 Demo MD Simulation SID analysis

[@rana.692]

great video. Thanks a million!

[@LaudvekkysGrooveLab]

My problem is the cms.file does not generate. So I dont have the T symbol there to load trajectory

[@CarolineMaina-e7o]

Thank you so much. 💝💞💕

[@SaraAshraf-d9o]

Which software are you using?

[@vikasgurjar7661]

I am facing problem with my schrodinger as a dummy host file in linux

[@fatimarida1065]

hello sir, i am facing an issue. my desmond_job.out.cms file is not generating? what should I do now?

[@nagavenicavuturu9179]

I have few queries regarding md desmond

[@亦雪蓝]

Excuse me, why do I click on run when I follow your video to calculate molecular dynamics? It will show that GPU is invalid.

[@Alchemist_of_India]

Try in another GPU...your gpu doesn't support

[@nagavenicavuturu9179]

How can I reach you

[@rajiniraja9566]

In LP contacts, How the ALA 213 makes 94% interaction, though it was a hydrophobic amino acid?

[@Alchemist_of_India]

It is forming H bond

[@wilberforcendarawit6705]

If I want access to Schrodinger how can I get one thank you

[@saturated3022]

You can’t get access of Schrödinger as it is not freely available
It is only provided by the institution or other research lab as it is very expensive software around I think 50-60 lakh and you must paid 10-15 lakh extra for Desmond module

[@uddalakdas]

How to do MMGBSA after MD simulations in GUI?

[@arfan3251]

i have the same question as you sir

[@srishtisrivastav1311]

After protein prepration how toh select ligand with which we want toh do simulation

[@harper8994]

Choose ligands from ligand library from online databases such as drugbank, Chembl, ChemSpider, ApexBio. Choose ligand based on their activity. Dock the protein and ligand and use the complex with highest binding score for the MD Simulation.

[@kolawoleabdulazeez3771]

​@@harper8994The complex will still show as a separate entry in Maestro

[@muhammadshahab1421]

Thank you sir for presenting this and sir how I install this software and does it work in simple system

[@Alchemist_of_India]

It's not free software

[@ES-yd1ze]

Geneus kushik

[@samrah-h4y]

My problem is the cms.file does not generate. So I dont have the T symbol there to load trajectory

[@samrah-h4y]

I am facing an issue. my desmond_job.out.cms file is not generating? what should I do now?