Messages

1

General discussions (Q&As) / mutate_bases error

« on: July 12, 2023, 03:05:59 pm »

Hello Sir,

Thank you for such a beautiful forum. I want to use mutate_bases to mutate the cytosine base pair. However, it shows this error.

$ mutate_bases -s fiber_model.pdb -m 4 5CM output.pdb
'mutate_bases' is not recognized as an internal or external command,
operable program or batch file.

Please help in understanding why I am getting this error.

Thank you

2

General discussions (Q&As) / installation error in MAC

« on: November 22, 2021, 02:16:43 pm »

I tried to install x3DNA in mac and it shows "-bash: final_pair:command not found".
I went to bin and clicked on x3dna set up and it showed that I need to copy export X3DNA and PATH to ~./bashrc file. I went to terminal and created a bashrc file and copied the above things. Now I tried to run source ~/.bashrc, I think it was successful but when I typed final_pair -h it shows error. Can you please help me in solving this error?

Thank you!

3

MD simulations / Re: generate DNA pdb file for Gromacs

« on: October 27, 2021, 01:00:46 pm »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

4

MD simulations / DNA step parameters

« on: October 27, 2021, 09:18:45 am »

I am an experimentalist working on DNA-drug binding. However, to support my result I am trying to do simulation. Since I don't have an experimentally determined structure for my custom 12-mer DNA duplex, I have to create one from scratch. I am using  w3dna.rutgers.edu,  to create a wide variety of nucleic acid structures.  However, I want to know what is base parameter file or where can I get that file.

I will really appreciate if you can please guide me.

Thank you for your help.