Topics

1

General discussions (Q&As) / Problem in .Out file

« on: June 15, 2007, 12:31:06 am »

hello sir
I carried simulations of DNA seq CGATCG alone using MOE s/w. when i converted the its .Pdb file into .Out file m getting only 3 base pairs
------------------------------------------------------------------------------------------------------------------------------------------
Number of base-pairs: 3
Number of atoms: 246
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.049) -:...4_:[..T]T-*---G[..G]:...8_:- (0.090)     |
   2   (0.080) -:...3_:[..A]A-*---A[..A]:...9_:- (0.059)     |
   3   (0.077) -:...2_:[..G]G-*---T[..T]:..10_:- (0.036)     |

Note: This structure contains 3[0] non-Watson-Crick base-pairs.
--------------------------------------------------------------------------------------------------------------------------------------------

Can you pls explain me y m gettng diffrnt results.

Regards,

Anju Sharma

2

General discussions (Q&As) / Problem while converting .Pdb file into .Out file

« on: June 12, 2007, 11:47:17 pm »

Hello Sir,
I have converted my .Pdb files into .Out files bt problem now m facing is wth .Out files. Now while carrying out the analysis work m facing a major problem. The DNA sequences i have given (present in .PDB files) and the one in . Out files are different. Example if in .Pdb file sequence is CGATCG thn in .Out file m getting CGATCC, also in many (almost all) if in .Pdb files there are 6 residues thn in .Out files m gettng either 4 or 3. how it is possble when the sequence is same then in some .Out files its showng jst 3 residues and in some 4 nd lk wise.

Waiting for early response, coz all work is at halt.

regards,

Anju Sharma

3

General discussions (Q&As) / Unable to generate .out file by using analyze command

« on: May 16, 2007, 01:57:52 am »

Hello

Please ignore the queries posted by me earlier to this. After reading similar prblms in d forum nd solutions provided to them i am able to convert my .pdb file to .inp file

But again m struck at next step, while trying to analyze my DNA seq using command:
# analyze atc.inp

no main parameter output file is generated (.out). where is the fault please do let me know.

files that are being generated are:
atc.inp                 bp_order.dat                   col_helices.scr                ref_frames.dat
auxiliary.par        bp_step.par                    hel_regions.pdb               stacking.pdb
bestpairs.pdb      cf_7methods.par            hstacking.pdb                
bp_helical.par      col_chains.scr               poc_haxis.r3d

4

General discussions (Q&As) / bash: find_pair: command not found

« on: May 16, 2007, 12:46:05 am »

Hello Sir,

While trying to convert my .pdb file to .inp i got following error. Please guide me how to overcome following problem. I'l b very thankful to you.

[root@amber bin]# set X3DNA /usr/local/X3DNA/X3DNA
[root@amber bin]# export PATH=$PATH:$X2DNA/bin
[root@amber bin]# echo $PATH
/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/amber8:/usr/local/moe/bin:/bin
[root@amber bin]# find_pair -t /usr/local/Anju/try/atc.pdb /usr/local/Anju/try/atc.inp
bash: find_pair: command not found
[root@amber bin]# which find_pair
/usr/bin/which: no find_pair in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/amber8:/usr/local/moe/bin:/bin)
[root@amber bin]#

5

General discussions (Q&As) / Problem while converting .pdb file into .inp file

« on: May 16, 2007, 12:32:08 am »

Hello Sir,
After compiling X3DNA on Linux and Solaris platform when i am tryng to convert my .pdb file to .inp file following error is encountered again and again. Could anyone please help me how to overcome or solve this problem.

Error:

[root@amber bin]# find_pair -t /usr/local/Anju/atc.pdb /usr/local/Anju/atc.inp

 ...... /root/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......
open_file </root/X3DNA/BASEPARS/misc_3dna.par> failed: No such file or directory[root@amber bin]#