Messages

1

General discussions (Q&As) / Re: stacking area overlap

« on: September 02, 2013, 11:44:00 am »

thanks dr Lu for the help..

2

General discussions (Q&As) / stacking area overlap

« on: September 02, 2013, 04:11:43 am »

Dear users,

I found that x3dna gives the stacking area overlap between base-pairs/steps. But that only includes are overlap between paired bases. If i want to calculate stacking area between single stranded base residues say consecutive bases in an RNA loop..can it be done in 3DNA?

Thank you

Asmita

3

General discussions (Q&As) / Re: dependency on GLIBC_2.14

« on: March 01, 2013, 01:28:15 pm »

This version is working perfectly.....and yes,  i was using a dec2012 version previously...

Thanks for the help Dr Xu...


Asmita

4

General discussions (Q&As) / Re: dependency on GLIBC_2.14

« on: March 01, 2013, 03:00:29 am »

Thanks for the response Dr Xu.

output of uname -a :

"Linux hostname 2.6.32-5-amd64 #1 SMP Fri Feb 15 15:39:52 UTC 2013 x86_64 GNU/Linux"

and of lsb_release -a :

Distributor ID: Debian
Description:    Debian GNU/Linux 6.0.7 (squeeze)
Release:        6.0.7
Codename:       squeeze

Asmita

5

General discussions (Q&As) / dependency on GLIBC_2.14

« on: February 28, 2013, 01:52:23 pm »

Dear Dr Xu,

  I am a Linux Debian user and have recently downloaded the latest x3dna-v2.1. when running the executables, i am getting this message :

"mutate_bases: /lib/libc.so.6: version `GLIBC_2.14' not found (required by mutate_bases)"

Now current debian distribution has 2.11 version, and there is no hope that future debian distributions will go for higher glibc versions.

Is it possible to run x3dna programs with this older version of glibc??

Thanks

Asmita

6

General discussions (Q&As) / Re: no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 06, 2012, 12:24:43 pm »

Dr Lu

    The issue i mentioned is coming in 2012 October beta v2.1 only...(for 64 bit ubuntu). As i am relatively new, i installed the latest version given in the downloads section in the first place....I am trying to reformat all the pdb files now...if it works then i'll post again


Asmita

7

General discussions (Q&As) / Re: no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 06, 2012, 06:57:55 am »

Dr Lu

   Thanks for the response...As you suggested, i made the changes in the atomlist.dat file...Find_pair seems to be working fine, but when i am running analyze -c on .inp files, i am getting this message :

-----------------------------------------------------
......Processing structure #1: <1l2x_prod_run_1.inp>......
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name ' C5', chain  , number [   1 ]
missing ' O1P' atom : residue name ' C5', chain  , number [   1 ]
missing ' O2P' atom : residue name ' C5', chain  , number [   1 ]
missing ' O1P' atom : residue name '  G', chain  , number [   2 ]
missing ' O2P' atom : residue name '  G', chain  , number [   2 ]
missing ' O1P' atom : residue name '  C', chain  , number [   3 ]
missing ' O2P' atom : residue name '  C', chain  , number [   3 ]
missing ' O1P' atom : residue name '  G', chain  , number [   4 ]
missing ' O2P' atom : residue name '  G', chain  , number [   4 ]
missing ' O1P' atom : residue name '  G', chain  , number [   5 ]
missing ' O2P' atom : residue name '  G', chain  , number [   5 ]
missing ' O1P' atom : residue name '  C', chain  , number [  24 ]
missing ' O2P' atom : residue name '  C', chain  , number [  24 ]
missing ' O1P' atom : residue name '  G', chain  , number [  25 ]
missing ' O2P' atom : residue name '  G', chain  , number [  25 ]
missing ' O1P' atom : residue name ' G3', chain  , number [  26 ]
missing ' O2P' atom : residue name ' G3', chain  , number [  26 ]
missing ' O1P' atom : residue name '  G', chain  , number [  16 ]
missing ' O2P' atom : residue name '  G', chain  , number [  16 ]

..
.
.
.
--------------------------------------------------------------------------------

As there are lakhs of PDB files, instead of formatting these files, i tried to introduce these modifications in atomlist.dat :
------------------------
.
.
.
OP..   O        (for OP1,OP2 etc)
O.P.   O        (for O1P, O2P etc)
..OP   O        (in case some weird naming convention comes up)
-------------------------

but still analyze -c run fails saying that "couldn't handle strand information" with error message mentioned above..could you please suggest what can i do?

Thanks

Asmita

8

General discussions (Q&As) / no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 05, 2012, 03:14:44 pm »

Dear Users,

   I am new to 3DNA suite of programs. I have a set of PDB coordinates generated using ptraj utility in Amber MD package. For the same i want to analyze base-step geometries. When i am running find_pair pdb-file pdb-file.inp and then analyze -c pdb-file.inp, an output file is generated , but when i am trying to do the same on multiple files using a shell script in a loop, i am getting this message :

-------------------------------------------------------------------------------------
no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
        check and update file $X3DNA/config/atomlist.dat
no matching entry for atom name [OP2 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
        check and update file $X3DNA/config/atomlist.dat
no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
-----------------------------------------------------------------------------------
 and hence analyze doesn't give an output file, saying "can not read strand information"

i tried to manually add the OP1, OP2 and O1P, O2P entries in atomlist.dat, but still getting the same message. What am i missing here? an example PDB file is attached herewith...

Thanks

Asmita