Krithika Unmesh

6 Questions 5 Answers 0 Followers

Questions related from Krithika Unmesh

Is there a way to generate stereo-isomers (R and S) of a cyclic peptide ?

I am working with a cyclic peptide and I would like to generate the stereo-isomers of my peptide. The stereo-centers are present in the ring. Is there a way I can do it, other than manually...

01 September 2023 7,180 0 View

Equilibrating a system by applying restraints in namd ?

Hi researchers, Can anyone help me to find out how we could equilibrate a system(step by step) by applying restraints to a desired set of heavy atoms using NAMD ? Thank you, Krithika.

17 November 2022 4,752 0 View

I encountered a fatal error during simulation of ATP using NAMD and VMD. Could anyone please help me rectify ?

I was performing the equilibration and minimization of ATP in namd and vmd. This is the error message. FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all27_na.rtf LINE=** \\\\...

17 January 2022 7,620 21 View

How to edit .pdb of an ATP molecule using 'atomselect' in tcl ?

My .pdb file is of a solvated ATP. I was trying to change the (res)name in the .pdb TIP3W to TIP using atomselect in tcl. But something is not working. I am confused how to select "TIP3W". I...

23 December 2021 946 4 View

Solvating a system using namd and vmd, with desired water box dimension and desired number of water molecules?

How can I create a water box around our system with desired dimensions with desired number of solvent molecules around it (say a 50A x 50A x 50A cubic box containing 1000 water moleclues.) using...

27 July 2021 2,781 4 View

How can we obtain an available force field parameter in GROMACS format?

While using pdb2gmx for ATP molecule, I encountered an error which shows, "Residue 'ATP' not found in residue topology database". So, I was trying to find force fields that natively supports ATP...

20 April 2021 8,645 5 View