Ashfaq Ahmad

5 Questions 29 Answers 0 Followers

Questions related from Ashfaq Ahmad

Problem in patching of Homodimeric template?

Hello All, I want to patch two templates into one. Each of it is a homodimer. They are; TMH and a periplasmic protein. There are no missing residues, and I want to patch them both into a single...

03 March 2018 7,651 9 View

How can we successfully call "STRIDE" by VMD?

I am using vmd-1.9.3. In Graphics ---> representation --> Drawing Method (New Cartoon) always result to a tube representation. I am having a two line error (see below), and it is important...

01 January 2018 1,948 0 View

How to do Constrain Minimization of Metallic Ions in Protein?

Hello Every one, I am trying to simulate a metalo-protein that harbor 2 Zinc ions in the active pocket. I am using the metalic force field of charmm. What i observed, after minimization both the...

06 June 2016 9,354 17 View

Did any one ever used metal topology file of CHARMM?

Hi Guys, I have wasted a complete day to solve this but failed. I am using "top_all22_prot_metals.inp" topology file to prepare PSF for a protein having 2 ZN ions. I have experience in NAMD,...

06 June 2016 2,855 6 View

NAMD execution on cluster?

Hello Every One, I am using NAMD for the last couple of years. Now I got a chance to use NAMD on cluster. To ask very simply, can any one provide me a kind of script.sh or tell me how to make...

06 June 2016 1,833 3 View