Messages

1

MD simulations / Re: Analysis of PDB file:query

« on: April 19, 2012, 08:44:40 am »

I modified the pds and now got 14 nos. of base pairs out of 15 ( I found there was some spacing problem in pdbs), thanks a lot, I am attaching the files.

2

MD simulations / Re: Analysis of PDB file:query

« on: April 18, 2012, 12:36:09 am »

there are 15 no.s of base pairs in each pdb, but I found in one case 9 and in another case 10 out of 15 pairs.

3

MD simulations / Analysis of PDB file:query

« on: April 17, 2012, 10:04:31 am »

Dear all,

I am using 3DNA for analysis of data, but I found the output files were not proper, are the pdb files not appropriate or something else, please suggest me, I am attaching two pdb files with this mail, please find those in attachments and suggest me.

Souvik 

4

MD simulations / Analysis of PDB file

« on: April 07, 2012, 03:35:08 am »

Hello Every one,

I tried to run "manalyze" using my pdb, but it was running, can you please suggest is there any problem in my pdb file, and I also want to generate the .out file. Please suggest me, I am attaching the pdb file.

regards & thanks,
SOUVIK

5

MD simulations / Re: Interpretation of Analysis data from 3DNA

« on: February 29, 2012, 02:05:47 am »

Please send me the link to download 3DNAv2beta version.

thanks

6

MD simulations / Re: Interpretation of Analysis data from 3DNA

« on: February 27, 2012, 08:53:09 am »

hello

please find the pdb file related to the .inp file, I have also "analyze" it and got some data but those data did not contain any backbone angle parameters.

7

MD simulations / Interpretation of Analysis data from 3DNA

« on: February 25, 2012, 01:46:59 pm »

Hello Everybody,

I have done some analysis in 3DNA, and got output files from it.
But cannot able to interpret it, can you please guide me for that, I am attaching output files,
And I also want backbone parameters to generate from 3DNA, how can I do this?
I shall be so grateful if you please suggest any reference paper regarding it.
Please do reply.

8

General discussions (Q&As) / PNA-DNA duplex study using 3DNA

« on: November 25, 2011, 10:47:39 pm »

Hello Everyone,

I have done MDsimulation of PNA(peptide nucleic acid)-DNA duplex using amber suite programme, so I got trajectory files and pdbs after simulation, now I am trying to analyze those pdbs  in 3DNA using find_pair command, but in everycase I found that it showed: no basepairs found, I cannot get it, Can you please suggest me in this regard.I am sending you my pdb of the duplex. Please let me know.

regards,
SOUVIK