Obinna Onyemaobi

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Questions related from Obinna Onyemaobi

I got this error message below while trying to generate a mol2 file using antechamber for graphene-glycine in one pdb file. what do i do?

"This molecule may have more than one unit. antechamber can only handle one unit. If the input is a single unit then the connectivity is wrong and the geometry may be bad....

16 December 2023 4,240 0 View

How can one identity the Mainchain-Mainchain and Mainchain-Sidechain in two interacting peptides and the number of strcutures attached to them?

after performing Hydrogen bond analysis using Ambertools

17 August 2023 5,139 0 View

How do i use MM/GBSA to calculate binding energy between two peptides after simulations in amber?

how to use MM/GBSA to calculate binding energy between two peptides after simulations in amber

22 July 2023 2,653 0 View

If two peptides are interacting and i want to apply restraint on the N-terminal of one of the peptide, what command line should i use in amber?

if two peptides are interacting and i want to apply restraint on the N-terminal of one of the peptide, what command line should i use in amber?

05 July 2023 6,118 0 View

If you want to applying restraint on the N-terminal of one of the two interacting peptides, how will the heating input file look like using amber?

i just want to confirm something before running my simulations?

05 July 2023 1,106 0 View

How can I put 2 independent protein structures in a single solvent box without any of them overlapping using Amber command line?

if there is an amber command line for that, how will it look like because the one i used made both peptides overlap

27 June 2023 3,187 5 View