Messages

1

General discussions (Q&As) / Re: PDB conversion

« on: June 07, 2017, 06:42:41 am »

I found the problem, mainly that I was working with mutated bases. It is still possible, but first you need to modify the file so it only contains the four canonical bases before running it through babel. Otherwise it doesn't recognise the molecule as DNA and just creates a generic PDB file.

2

General discussions (Q&As) / Re: PDB conversion

« on: May 31, 2017, 04:26:59 am »

Thanks, that does confirm what I had suspected. However I still don't have a way to create the correct PDB format from XYZ files. I suppose I could try change the file manually but that doesn't seem like an efficient way to do things, given this is something I will have to do many times. Is there a function in 3DNA that will do this? Or is there a program other than openbabel that does the conversion properly?

3

General discussions (Q&As) / PDB conversion

« on: May 29, 2017, 06:49:35 am »

Hi Xiangjun

I am having trouble with XYZ files converted to PDB format using OpenBabel, the XYZ files come from gaussian 09 optimised structures. Whenever I try using the converted PDB file with find_pair, I always get the message that there are no base pairs. The converted files open normally in viewers like avogadro, so I don't think there should be any issues from the conversion process. I see a similar topic was raised (Conversions, jterry0402) but not pursued. I have attached both the original and converted files.