Topics

1

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

2

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

3

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