VMD-L Mailing List

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Mon Aug 06 2007 - 14:27:52 CDT

Hello,
Thank you for your reply. First off, a some history on how the .pdb
file that I am using came into being. My initial hope was to find a
program or tool that would be able to build .pdb's for a specified
sequences of bases to yield a single stranded RNA. The issues that I
had with this approach are delineated in:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6145.html

After several unsuccessful attempts to build a .pdb file for a
specific single stranded RNA sequence and having not tried nucgen in
AMBER as you suggested, I made a single stranded 3 nucleotide long pdb
file starting from:
http://www.pdb.org/pdb/explore/explore.do?structureId=420D

I deleted the second strand and most of the nucleotides on the first
strand, and was left with the first three nucleotides. I then added
the missing hydrogens to neutralize the O- on the phosphate and
alcohol groups at the end of the pdb file. I used VMD to confirm that
the locations of the H's were realistic. I am pasting the part of the
file that I made changes to below. The rest (remarks section, etc)
are the same as
http://www.pdb.org/pdb/explore/explore.do?structureId=420D.

Thank you again for your help.

Audrey

DBREF 420D A 1 16 AR0006 1 16
SEQRES 1 A 16 G C A G A G U U A A A U C

CRYST1 42.530 42.530 128.060 90.00 90.00 120.00 R 3
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023513 0.013575 0.000000 0.00000
SCALE2 0.000000 0.027150 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007809 0.00000
ATOM 1 O5* G A 1 1.042 13.763 21.926 1.00 36.88 O
ATOM 2 C5* G A 1 -0.213 14.389 21.639 1.00 30.42 C
ATOM 3 C4* G A 1 -0.263 15.762 22.262 1.00 32.10 C
ATOM 4 O4* G A 1 0.258 15.655 23.606 1.00 27.76 O
ATOM 5 C3* G A 1 0.614 16.811 21.599 1.00 33.87 C
ATOM 6 O3* G A 1 -0.078 17.451 20.531 1.00 46.64 O
ATOM 7 C2* G A 1 0.891 17.771 22.745 1.00 28.19 C
ATOM 8 O2* G A 1 -0.173 18.665 22.978 1.00 33.49 O
ATOM 9 C1* G A 1 1.021 16.801 23.919 1.00 25.47 C
ATOM 10 N9 G A 1 2.387 16.355 24.146 1.00 20.12 N
ATOM 11 C8 G A 1 2.875 15.081 23.987 1.00 19.67 C
ATOM 12 N7 G A 1 4.146 14.983 24.271 1.00 24.45 N
ATOM 13 C5 G A 1 4.515 16.274 24.639 1.00 24.75 C
ATOM 14 C6 G A 1 5.773 16.794 25.063 1.00 21.56 C
ATOM 15 O6 G A 1 6.849 16.199 25.203 1.00 24.75 O
ATOM 16 N1 G A 1 5.695 18.154 25.336 1.00 23.99 N
ATOM 17 C2 G A 1 4.559 18.918 25.220 1.00 23.83 C
ATOM 18 N2 G A 1 4.675 20.221 25.539 1.00 31.32 N
ATOM 19 N3 G A 1 3.390 18.447 24.825 1.00 25.49 N
ATOM 20 C4 G A 1 3.440 17.130 24.560 1.00 18.72 C
ATOM 21 P C A 2 0.643 17.619 19.101 1.00 47.83 P
ATOM 22 O1P C A 2 -0.386 17.897 18.064 1.00 46.50 O
ATOM 23 O2P C A 2 1.556 16.457 18.941 1.00 54.49 O
ATOM 24 O5* C A 2 1.544 18.914 19.276 1.00 37.58 O
ATOM 25 C5* C A 2 0.949 20.173 19.579 1.00 32.04 C
ATOM 26 C4* C A 2 1.981 21.086 20.171 1.00 37.84 C
ATOM 27 O4* C A 2 2.498 20.477 21.387 1.00 41.05 O
ATOM 28 C3* C A 2 3.240 21.270 19.343 1.00 41.36 C
ATOM 29 O3* C A 2 3.076 22.199 18.287 1.00 42.91 O
ATOM 30 C2* C A 2 4.221 21.769 20.392 1.00 41.50 C
ATOM 31 O2* C A 2 4.020 23.136 20.719 1.00 42.90 O
ATOM 32 C1* C A 2 3.855 20.863 21.571 1.00 37.06 C
ATOM 33 N1 C A 2 4.674 19.648 21.603 1.00 26.45 N
ATOM 34 C2 C A 2 5.961 19.728 22.125 1.00 24.98 C
ATOM 35 O2 C A 2 6.379 20.826 22.525 1.00 23.55 O
ATOM 36 N3 C A 2 6.722 18.614 22.179 1.00 26.71 N
ATOM 37 C4 C A 2 6.240 17.457 21.723 1.00 25.47 C
ATOM 38 N4 C A 2 7.026 16.378 21.809 1.00 27.11 N
ATOM 39 C5 C A 2 4.934 17.352 21.164 1.00 24.89 C
ATOM 40 C6 C A 2 4.190 18.463 21.129 1.00 22.65 C
ATOM 41 P A A 3 3.899 21.990 16.925 1.00 40.06 P
ATOM 42 O1P A A 3 3.360 22.975 15.955 1.00 46.10 O
ATOM 43 O2P A A 3 3.897 20.536 16.584 1.00 34.33 O
ATOM 44 O5* A A 3 5.384 22.417 17.315 1.00 36.13 O
ATOM 45 C5* A A 3 5.671 23.773 17.675 1.00 35.24 C
ATOM 46 C4* A A 3 7.084 23.898 18.176 1.00 39.19 C
ATOM 47 O4* A A 3 7.240 23.170 19.428 1.00 41.98 O
ATOM 48 C3* A A 3 8.156 23.281 17.306 1.00 37.95 C
ATOM 49 O3* A A 3 8.473 24.065 16.175 1.00 40.95 O
ATOM 50 C2* A A 3 9.302 23.197 18.297 1.00 35.99 C
ATOM 51 O2* A A 3 9.828 24.475 18.601 1.00 35.81 O
ATOM 52 C1* A A 3 8.560 22.648 19.512 1.00 35.76 C
ATOM 53 N9 A A 3 8.478 21.193 19.426 1.00 29.39 N
ATOM 54 C8 A A 3 7.437 20.425 18.968 1.00 27.40 C
ATOM 55 N7 A A 3 7.681 19.137 18.986 1.00 24.13 N
ATOM 56 C5 A A 3 8.969 19.050 19.495 1.00 25.01 C
ATOM 57 C6 A A 3 9.812 17.954 19.764 1.00 24.17 C
ATOM 58 N6 A A 3 9.478 16.681 19.526 1.00 19.75 N
ATOM 59 N1 A A 3 11.029 18.214 20.288 1.00 24.50 N
ATOM 60 C2 A A 3 11.374 19.490 20.508 1.00 26.96 C
ATOM 61 N3 A A 3 10.675 20.605 20.287 1.00 27.45 N
ATOM 62 C4 A A 3 9.468 20.310 19.777 1.00 28.12 C
ATOM 63 H2* G A 1 -0.300 19.665 22.978 1.00 1.00 H
ATOM 64 H2* C A 2 4.500 24.136 20.719 1.00 42.90 H
ATOM 65 H2* A A 3 10.83 24.800 18.601 1.00 35.81 H
ATOM 66 H3* A A 3 9.473 24.065 16.175 1.00 40.95 H
ATOM 67 H5* G A 1 2.042 13.763 21.926 1.00 36.88 H

TER 67 A A 4
MASTER 230 0 1 0 0 0 0 6 735 2 0 4
END

On 8/6/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Audrey,
> as an aside, if the chain splitting that autopsf comes up with seems odd
> to you, I'd appreciate it if you could send me your pdb, along with what
> you would intuitively expect to be the chain identities, so I can see
> why the splitting is not intuitive. And certainly, as Axel noted,
> suggestions for the documentation are also welcome.
> Thanks,
> Peter
>
> 

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA