Udhaya Kumar

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Questions related from Udhaya Kumar

Is there a Gromacs Tutorial to add a residues to a force field and modifying a .rtp, .itp, atomtypes.atp and residuetypes.dat file?

If anyone have gromacs tutorial to a new residue to the topology. The protein which I am working on has 4 NAG (N-acetyl Glucosamine) and 1 ALS (2-amino 3-oxopropionic acid). These residues were...

16 June 2015 2,255 3 View

Why do I get huge fluctuations in RMSD when I simulate a protein in 20ns using Amber99sb force field in Gromacs 5.0.4?

I have followed the "Tutorial for Trypsin-‐Benzamidine complex molecular dynamicsstudy" (pdf file attached below) and some of the inputs i have changed according to my protein name and ligand...

05 March 2015 3,731 7 View