Messages

1

General discussions (Q&As) / Re: How to get structural parameters from find_pair?

« on: March 25, 2012, 10:31:46 am »

Xiang-Jun-

Fixing the atoms names did indeed fix my problem.  find_pair now works correctly on the cases I have tested so far.

I have made some OpenBabel-formatted pdb files from Gaussian outputs with all 5 nucleobases.  Due to some technical issues they are not actually basepairing; the coordinates are just all there in the file.  As I was creating these I found that OpenBabel is actually more clever than I had originally believed: if the entire base is there in the Gaussian output (with sugar included) then OpenBabel will correctly format the PDB with atoms names/residue names, etc.  It is only in cases where parts have been changed (as when I replaced the sugar ring with a methyl group) that OpenBabel reverts to the default "LIG" for "ATOM" and default atom names, etc.

In my situation I still needed a way to get the correct atom names into a number of pdbs though, so I have written a perl script that can do this.  It works for all of the nucleobases and can handle an arbitrary number of them.   I have done only limited testing on it so far, so if I find other bugs I will post corrections to this thread.  I have taken a cue from the x3dna2charmm_pdb script for the usage line :-)  If this script is useful to others they can feel free to use/change it, but I don't know how many other people will face the same situation as me.

I will go ahead and post the OpenBabel pdbs too.

-Hugh

2

General discussions (Q&As) / Re: How to get structural parameters from find_pair?

« on: March 23, 2012, 02:56:44 pm »

Xiang-Jun,

Thank you for the very prompt reply.  I will modify my pdb to have the correct atom names and will try again.  Also, I will work to provide you with the files that you have requested.

-Hugh

3

General discussions (Q&As) / How to get structural parameters from find_pair?

« on: March 23, 2012, 10:19:28 am »

Hello Dr. Lu and other users,

I am a very new user of 3DNA.  I have done some simulations of RNA and have found some examples of interesting base pairs in them.  Now I would like to search the PDB for other examples of these types of base pairs.  3DNA looks like it could be a very useful tool to accomplish this.

Like the user in this post: http://forum.x3dna.org/general-discussions/analyzing-a-pdb-containing-isolated-bases/msg35/#msg35 I have used Gaussian to optimize the gas phase structure of my base pair.  I have replaced everything beyond the glycosidic bond with a methyl group.  I have tried both Gaussview and OpenBabel to get my Gaussian output file into pdb format.  Some information is missing since Gaussian does not know/care about residue type, etc.  I have tried to add some of this information/reformat by hand, but I still worry that I do not have a correctly formatted file.

When I run find_pair with the options -pz on my pdb file, it does not find any pairs.  I suspect this is a formatting issue, although I do not hear any complaints from find_pair about missing fields (as I did when trying to run find_pair on the pdb file produced by Gaussview).

So I guess I have two questions:

1. Is the attached file properly formatted for use with 3DNA?

2. If find_pair does not find a base pair, will it still output the base pair geometry parameters that were calculated?  This would be very useful to me, because I believe that some of the base pairs I would like to search for may be outside of the default parameters.  This would tell me automatically how I should change 3DNA's base pair parameters to search the pdb for other examples.

Thanks!
-Hugh Heldenbrand
Graduate Student, U of MN