VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 06 2007 - 15:59:17 CDT

Hi Audrey,
several of the hydrogens at the end of the file are not included in
their parent residues; you have hydrogens from residues 1, 2, 3, and
then 1 again. This is confusing the chain splitter, which thinks that if
your residue number drops, it must mean a new chain started. If you edit
your file to have the hydrogen atoms come immediately after their parent
residues, it should work as you expect.
Peter

Audrey Salazar wrote:
> 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
>>
>>
>>
>
>
>