Subhanjan Majumder

5 Questions 6 Answers 0 Followers

Questions related from Subhanjan Majumder

I want to do a simulation of a tRNA containing GDP and/or GMP , GTP as one of its bases. How do I load this structure in AMBER11 and/or NAMD2.9 ?

I want to do a simulation of a tRNA containing GDP and/or GMP , GTP as one of its bases. How do I load this structure in AMBER11 and/or NAMD2.9 ? Please suggest.

18 August 2019 3,226 0 View

I have some problem regarding parametrization of Perchlorate ion in Antechamber.

I have some problem regarding parametrization of Perchlorate ion. I can't generate .frcmod and .mol2 file in antechamber. Can anyone help me regarding this?

01 January 1970 2,118 3 View

RESP charge for Cu2+ ion.

I want to get an RESP charge for Cu2 + ion. Can anyone help me with how to get the RESP charge and to create topological files (mol2 and frcmod) for amber simulation using RESP charge data.

01 January 1970 6,063 2 View

How to add parameters of Cu+2 in NAMD?

I am new to NAMD. I have to run a simulation for a system having a macromolecule containing Cu+2 ion. I have generated psf files for the macromolecules but couldn't find an appropriate parameter...

01 January 1970 5,775 0 View

How to do manual parameterization in AMBER11?

I am unable to generate parameter for iodide ion in tleap of amber. Amber parameter database doesn't have parameter for it. The force field I am using is ff99SB. Kindly suggest how I can go about...

01 January 1970 1,158 4 View