Udhaya Kumar

6 Questions 16 Answers 0 Followers

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...

06 June 2015 2,178 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...

03 March 2015 6,089 7 View

How to include the residues N-acetyl Glucosamine (NAG) and 2-amino 3-oxopropionic acid (ALS) in gromacs 4.6.5 version's topology ?

My protein has 4 NAG and 1 ALS residue in its sequence. When I tried to simulate the protein using gromos96 53 a6 force field , it's showing a fatal error as: residue 'ALS' not found in residue...

01 January 2015 6,065 4 View

How to install Tinker (Molecular design software) in ubuntu 14.04 version ?

TINKER is a molecular modelling software, the user guide is difficult to understand and install the software. Have any of you installed it before ? I need the detailed steps for installation. Any...

12 December 2014 6,294 3 View

Can anyone tell how to install gromacs on Ubuntu 14.04 ?

I am using ubuntu 14.04 version, please tell me which version of GROMACS I have to use for this ubuntu 14.04 version. And give me the Installation steps. I have installed cmake and c++98 compiler.

12 December 2014 7,249 4 View

What are the installation and simulation procedures for the AMBER tool?

See above

05 May 2014 976 1 View