Messages

1

General discussions (Q&As) / Re: DNA extending

« on: July 13, 2014, 01:41:11 pm »

Dear Xiang-Jun,

I can extend my dsdna pdb file. but the problem is all of Hydrogen atoms are missed in my new pdb file. Although there were Hydrogen atoms in my premier pdb file. I just want to know if there is any way to built pdb file containing Hydrogen atoms.

Thanks in advance,

Marzieh

2

General discussions (Q&As) / Re: DNA extending

« on: July 07, 2014, 02:02:03 pm »

Dear Xiang-Jun,

Thank you again. I've also used "find_pair" command at first, but without "stdout" at its end. Seems that it works now!

Best,

Marzieh

3

General discussions (Q&As) / Re: DNA extending

« on: July 06, 2014, 11:10:48 pm »

Hi dear Xiangjun,

First of all, thank you for all your guides and hints....

I have a question and I'll be so grateful if you could help me!
I'm quite new  in using x3dna. I wanna extend an ideal dsdna file(attached) from its 3' and 5' ends. My PDB has originally 40 bps, I wanna to extend it to 200 bps. I've just used the method you described below, but when I typed: "frame_mol -40 ref_frames.dat dsdna.pdb dsdna_ref40.pdb", I received an error "error reading parameter file (number of base-pairs): dsdna.pdb"
Could you please help me?

Best,
Marzieh