Messages

1

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 21, 2008, 10:04:53 pm »

Dear Dr. Lu,

With your help I have calculated the helical parameters of the xdna.


Thank you verymuch for your help.


Mathew

2

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 14, 2008, 01:47:15 am »

Dear Dr.Lu,

Thanks for your reply.
Hope that you will look into the XDNA parameters calculation

Thanks in advace

Mathew

3

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 04, 2008, 07:51:16 am »

Hi Xiangjun,

Thanks for your detailed reply.
I am attaching herewith the Atomic_?.pdb, which are taken from the xDNA by just taking the coordiantes of the modified bases. (I have added xae,xga,xcs and xty with the files to distingish them. In baselist.dat the name is only Atomic_X.pdb etc.)
In some of the xDNA papers, The authors   used 3dna and curves for calculating the the helical parameters. In the case of curves, the atom which is connected to the   C1' is just converted to nitrogen and renamed it to N1. Is this a valid thing to do?  

Thanks for you help.

Mathew

4

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 03, 2008, 12:54:31 am »

Hi,

I am sending my pdb file of the modified nuclic acid, baselist.dat, and input file created with find_pair.
I have given names W, X, Y, and Z for the modified bases and added Atomic_X.pdb, Atomic_Y.pdb etc. in the BASEPAIRS directory.
Thes files were extracted from the pdb file of the molecle, by taking just the coordinates of the corresponding bases.


I have edited the cent.inp file to include the missing basepairs and tried to run analyse. Here I got an error message that an unknown residue in the chain 1
------------------------------------------------------------------------
......Processing structure #1: <cent02.inp>......

 ...... /usr/people/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......

 ...... /usr/people/X3DNA/BASEPARS/ ......
 ...... reading file: baselist.dat ......
Non-base: residue XT5    1  on chain   [#1]
-----------------------------------------------------------------------

Looking forward to your help,

Thanking you,

Mahew

5

General discussions (Q&As) / helical Parameters of a Modified nucleic acids

« on: February 02, 2008, 12:18:57 pm »

Hi,
I am trying to calculate the helical parameters of a modified nucleic acid xDNA, which contains 4 modified bases and the normal bases.
Each modified base contains an additional bezene ring. I ahve tried the suggestion for adding the entry for additional bases in baselist.dat file. Atomic_X.pdb files for each new entry were added in the BASEPAIRS directory. Modified adenines and Guanines were identified by the program, but the modified Thymine and Cytosine were not identified.Modified ADE and GUA have same connection atom with the sugar, but the connection atom name is different for CYT and THY. I have also tried by modified ADE as A, GUA as G etc. Here also the purines were identified and pyrimidines were not.How can I make the program identify the new residues?

 
Thanking You for your help,

Mathew