3DNA Forum

Questions and answers => MD simulations => Topic started by: shynomat on May 29, 2012, 06:12:12 pm

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Title: pdb files created using v 1.5 and v 2.1 beta
Post by: shynomat on May 29, 2012, 06:12:12 pm
Dear users,

Initially I was using X3DNA v 1.5 for creating a pdb file, which I used for studying mutations.
Only recently I realized there are new versions of X3DNA and I tried creating the same pdb file using v 2.1 beta.
These two files seems to be different. Can anyone comment on this? does it mean the pdb file I created using v1.5 is not good?

Thank you very much,
Shyno Mathew
Title: Re: pdb files created using v 1.5 and v 2.1 beta
Post by: shynomat on May 29, 2012, 06:20:34 pm
To be more clear about my previous question, I used the 'diff' command to see if these structures are different.
But when I loaded both structures in vmd, they looked the same.
thanks
Shyno
Title: Re: pdb files created using v 1.5 and v 2.1 beta
Post by: xiangjun on May 29, 2012, 09:03:44 pm
To be clearer and more specific, please attach two PDB files you generated with 3DNA v1.5 and v2.1. What's your concern regarding the two PDB files? Overall, the v2.1 version is supposed to be more standard compliant, but the xyz coordinates should be the same.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.