different geometries

[angelo757]

Hi!

I have two molden file, each with a particular geometry of a nucleobase. I would like to get the coordinate of the system composed by these two nucleobases (in my particular geometries) orientated as in a B-DNA chain. How can i do that with 3dna?

thank you!

[xiangjun]

Thanks for using 3DNA and posting your question on the forum!

Could you be more specific by providing a concreate example to show us what a molden file look like?

Xiang-Jun

[angelo757]

Hi

a molden file contains a number equal to the number of atoms and then the coordinates. Here an example:
 
  15

 C     1.397720    -2.058510     0.380870
 C     0.217920    -2.704680     0.347260
 C    -0.714490    -2.367180    -0.746130
 N    -0.264230    -1.402130    -1.634910
 C     0.943010    -0.739230    -1.602440
 N     1.753070    -1.105070    -0.560170
 C    -0.201800    -3.743170     1.349530
 O    -1.794930    -2.871900    -0.889730
 O     1.251680     0.083850    -2.416570
 H    -1.119870    -3.442600     1.850390
 H    -0.394610    -4.694570     0.857760
 H     0.574230    -3.886580     2.097710
 H    -0.877580    -1.155340    -2.386380
 H     2.633990    -0.640570    -0.509790
 H     2.136440    -2.244190     1.142020

Thanks

[xiangjun]

Thanks for posting back an example molden file which help clarify the issue. No, that's not the format recognized by 3DNA programs. Currently, 3DNA only accepts PDB format file (coordinate record descriptions) as documented in the RCSB website. That said, it's feasible to convert your molden file via a purpose-oriented script or third-party utility -- Google search may help.

Xiang-Jun

[angelo757]

Ok, i can actually convert my files in PDB ones. For example i can easily convert the following molden file:

13

 N     -0.27027  -2.52902  -0.07647
 N     -0.30933   1.51866   0.00852
 N      0.86901  -0.54557   0.00442
 C     -0.26428  -1.15421  -0.01193
 C     -1.55706  -0.47298  -0.01607
 C      0.90709   0.84743   0.00653
 C     -1.51916   0.87341  -0.00349
 O      1.93530   1.46263   0.01428
 H      0.61273  -2.94719   0.14838
 H     -2.48328  -1.02141  -0.04004
 H     -2.39932   1.49728  -0.00681
 H     -1.05544  -2.98429   0.34380
 H     -0.26099   2.51631   0.01212

 in the following pdb file:

HEADER
HETATM    1  N     2     2      -0.270  -2.529  -0.076
HETATM    2  N     2     2      -0.309   1.519   0.009
HETATM    3  N     2     2       0.869  -0.546   0.004
HETATM    4  C     2     2      -0.264  -1.154  -0.012
HETATM    5  C     2     2      -1.557  -0.473  -0.016
HETATM    6  C     2     2       0.907   0.847   0.007
HETATM    7  C     2     2      -1.519   0.873  -0.003
HETATM    8  O     2     2       1.935   1.463   0.014
HETATM    9  H     2     2       0.613  -2.947   0.148
HETATM   10  H     2     2      -2.483  -1.021  -0.040
HETATM   11  H     2     2      -2.399   1.497  -0.007
HETATM   12  H     2     2      -1.055  -2.984   0.344
HETATM   13  H     2     2      -0.261   2.516   0.012

Having my two geometries in two such files, it is now possible to perform the task that i described in my first message?

Thanks

[xiangjun]

It's closer, but still not a proper PDB format -- see the thread "how the cartesian coordinates transform to PDB format" for details.

Given the fact that this issue has popped up quite a few times over the years, I may consider adding support in 3DNA to make such conversion more straightforward.

Xiang-Jun

[angelo757]

Just one little question. What an .rpt file contains?

thanks for your help

[xiangjun]

Could you be more specific by providing an example to put your question in context?

Xiang-Jun