Fatemeh Fadaei

6 Questions 7 Answers 0 Followers

Questions related from Fatemeh Fadaei

The issue with correcting PBC for DNA Separation in GROMACS?

Hello, I am trying to correct PBC for a DNA system, but even after running the commands, I still see artifacts in the trajectory. Here’s what I did: gmx trjconv -pbc whole -f traj.xtc -o...

12 January 2025 9,628 1 View

Fix two separate DNA strands in gromacs using -pbc cluster?

hello, I have used these two commands to fix two separate DNA strands. gmx trjconv -f file.xtc -s file.tpr -pbc cluster -o file-cluster.xtc gmx trjconv -f file-cluster.xtc -s file.tpr -pbc mol...

22 July 2024 1,062 3 View

Is there any online webserver for DNA-ligand docking?

I tried the following website. It does not work http://www.scfbio-iitd.res.in/dock/dnadock.jsp

23 October 2023 5,361 2 View

Query Regarding PDB2GMX Error with Amber Force Field?

I am currently working on DNA construction using the 3xDNA web server. I have encountered an issue when attempting to save the constructed DNA as a PDB and subsequently applying the Amber force...

30 September 2023 2,164 1 View

Generating PDB file for custom DNA sequence?

Given that the nab module is no longer available in the new AMBERTools, are there alternative software tools or methods for constructing circular DNA structures that are compatible with the AMBER...

27 September 2023 3,222 0 View

How can I resolve the issue of the 'NAB' command not being found in AmberTools23?

I am writing to seek assistance with an issue I have encountered while using AmberTools23 on my Ubuntu 23.04 system. Specifically, I am experiencing problems with the 'nab' command, which does not...

19 September 2023 9,353 1 View