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 ? Please suggest.
18 August 2019 3,222 0 View
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 2,105 3 View
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 6,058 2 View
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 5,771 0 View
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 1,154 4 View