Gauri Thapa

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Questions related from Gauri Thapa

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

11 February 2021 4,423 2 View

How to include MG topology information using pdb2gmx ?

I have a molecule with MG ions in the pdb file. When I am creating topology file using pdb2gmx, it does not recognize the MG ions (with gromos 54a7 ff). So I created pdb with only protein atoms...

24 January 2020 1,246 2 View

How to check the parameters generated by ATB for ligand molecule in gromacs?

I have generated parameters for Doxorubicin using ATB server to be used with gromacs. I have calculated solvation free energy of doxorubicin (parameters generated by ATB) which gives a value...

01 January 2020 6,172 3 View

How long does ATB server take to process the molecule submitted and give back the parameters ?

Can anyone give me a rough estimate of time it takes for ATB (gromacs)server to give the parameters for the submitted molecule ?

01 January 2020 4,536 3 View

How long does ATB server take to process the molecule submitted and give back the parameters ?

Can anyone give me a rough estimate of time it takes for ATB (gromacs)server to give the parameters for the submitted molecule ?

01 January 2020 745 3 View