Re: what is wrong with this pdb to simulate with NAMD

From: raghav singh (raghavbioinfo_at_gmail.com)
Date: Fri Oct 14 2011 - 12:04:20 CDT

On Fri, Oct 14, 2011 at 5:15 PM, raghav singh <raghavbioinfo_at_gmail.com>wrote:

> Hello All,
>
> I am using an i-motif structure which I have produced using rcsb pdb code
> 225D. when I used autopsfgen to generate psf and pdb file the results
> were disaster. can anyone suggest me what is wrong with this pdb?
>
>
> Before psfgen...(input)
> ATOM 1 P T A 1 72.387-257.674 29.870 1.00 .00
> ATOM 2 OP1 T A 1 72.217-258.288 28.392 1.00 .00
> ATOM 3 OP2 T A 1 71.090-256.764 30.161 1.00 .00
> ATOM 4 O5' T A 1 73.554-256.588 29.648 1.00 .00
> ATOM 5 C5' T A 1 74.286-256.063 30.742 1.00 .00
> ATOM 6 C4' T A 1 75.352-255.060 30.291 1.00 .00
> ATOM 7 O4' T A 1 76.441-255.677 29.624 1.00 .00
> ATOM 8 C1' T A 1 77.056-254.706 28.786 1.00 .00
> ATOM 9 N1 T A 1 77.164-255.263 27.434 1.00 .00
> ATOM 10 C6 T A 1 75.888-255.640 26.801 1.00 .00
> ATOM 11 C5 T A 1 75.988-256.303 25.421 1.00 .00
> ATOM 12 C7 T A 1 74.724-256.008 24.596 1.00 .00
> ATOM 13 C4 T A 1 77.296-255.972 24.707 1.00 .00
> ATOM 14 O4 T A 1 77.414-256.072 23.490 1.00 .00
> ATOM 15 N3 T A 1 78.381-255.603 25.451 1.00 .00
> ATOM 16 C2 T A 1 78.350-255.312 26.791 1.00 .00
> ATOM 17 O2 T A 1 79.434-255.105 27.328 1.00 .00
> ATOM 18 C3' T A 1 74.825-253.987 29.343 1.00 .00
> ATOM 19 C2' T A 1 76.158-253.452 28.828 1.00 .00
> ATOM 20 O3' T A 1 74.025-253.069 30.053 1.00 .00
> ATOM 21 P C A 2 73.231-251.877 29.311 1.00 .00
> ATOM 22 OP1 C A 2 71.882-251.764 29.908 1.00 .00
> ATOM 23 OP2 C A 2 73.410-252.028 27.848 1.00 .00
> ATOM 24 O5' C A 2 74.116-250.631 29.782 1.00 .00
> ATOM 25 C5' C A 2 74.339-250.360 31.154 1.00 .00
> ATOM 26 C4' C A 2 75.246-249.136 31.337 1.00 .00
> ATOM 27 O4' C A 2 76.489-249.303 30.659 1.00 .00
> ATOM 28 C1' C A 2 76.694-248.205 29.788 1.00 .00
> ATOM 29 N1 C A 2 76.522-248.663 28.386 1.00 .00
> ATOM 30 C6 C A 2 75.292-248.855 27.783 1.00 .00
> ATOM 31 C5 C A 2 75.204-249.234 26.488 1.00 .00
> ATOM 32 C4 C A 2 76.440-249.365 25.782 1.00 .00
> ATOM 33 N4 C A 2 76.496-249.520 24.474 1.00 .00
> ATOM 34 N3 C A 2 77.620-249.211 26.364 1.00 .00
> ATOM 35 C2 C A 2 77.693-248.867 27.668 1.00 .00
> ATOM 36 O2 C A 2 78.798-248.735 28.185 1.00 .00
> ATOM 37 C3' C A 2 74.588-247.831 30.876 1.00 .00
> ATOM 38 C2' C A 2 75.736-247.097 30.193 1.00 .00
> ATOM 39 O3' C A 2 74.081-247.112 31.979 1.00 .00
> ATOM 40 P C A 3 73.261-245.742 31.768 1.00 .00
> (this is just the initial part of the file)
>
> output
>
> REMARK original generated coordinate pdb file
> ATOM 1 C4' THY A 0 81.161-214.671 20.998 1.00 0.00 N1
> C
> ATOM 2 H4' THY A 0 81.484-214.572 21.939 0.00 0.00 N1
> H
> ATOM 3 O4' THY A 0 79.769-214.389 20.954 1.00 0.00 N1
> O
> ATOM 4 C1' THY A 0 79.116-215.442 21.637 1.00 0.00 N1
> C
> ATOM 5 H1' THY A 0 79.151-215.231 22.614 0.00 0.00 N1
> H
> ATOM 6 C2' THY A 0 79.961-216.691 21.365 1.00 0.00 N1
> C
> ATOM 7 H2' THY A 0 80.254-217.059 22.247 0.00 0.00 N1
> H
> ATOM 8 H2'' THY A 0 79.436-217.288 20.759 0.00 0.00 N1
> H
> ATOM 9 C3' THY A 0 81.188-216.169 20.611 1.00 0.00 N1
> C
> ATOM 10 H3' THY A 0 81.031-216.254 19.627 0.00 0.00 N1
> H
> ATOM 11 O3' THY A 0 82.367-216.879 20.986 1.00 0.00 N1
> O
> ATOM 12 H3T THY A 0 82.233-217.807 21.191 0.00 0.00 N1
> H
> ATOM 13 H5T THY A 0 82.380-211.738 20.050 0.00 0.00 N1
> H
> ATOM 14 O5' THY A 0 81.886-212.365 20.652 1.00 0.00 N1
> O
> ATOM 15 C5' THY A 0 81.919-213.676 20.087 1.00 0.00 N1
> C
> ATOM 16 H5' THY A 0 82.865-214.001 20.073 0.00 0.00 N1
> H
> ATOM 17 H5'' THY A 0 81.412-213.672 19.225 0.00 0.00 N1
> H
> ATOM 18 N1 THY A 0 77.733-215.594 21.128 1.00 0.00 N1
> N
> ATOM 19 C6 THY A 0 77.464-215.617 19.776 1.00 0.00 N1
> C
> ATOM 20 H6 THY A 0 78.068-215.474 18.992 0.00 0.00 N1
> H
> ATOM 21 C2 THY A 0 76.721-215.803 22.071 1.00 0.00 N1
> C
> ATOM 22 O2 THY A 0 76.950-215.704 23.278 1.00 0.00 N1
> O
> ATOM 23 N3 THY A 0 75.466-216.092 21.625 1.00 0.00 N1
> N
> ATOM 24 H3 THY A 0 74.636-216.310 22.298 0.00 0.00 N1
> H
> ATOM 25 C4 THY A 0 75.203-216.119 20.320 1.00 0.00 N1
> C
> ATOM 26 O4 THY A 0 66.008-186.836 18.799 1.00 0.00 N1
> O
> ATOM 27 C5 THY A 0 76.209-215.865 19.326 1.00 0.00 N1
> C
> ATOM 28 C5M THY A 0 75.886-215.875 17.861 0.00 0.00 N1
> C
> ATOM 29 H51 THY A 0 76.719-215.678 17.343 0.00 0.00 N1
> H
> ATOM 30 H52 THY A 0 75.232-215.132 17.722 0.00 0.00 N1
> H
> ATOM 31 H53 THY A 0 75.513-216.715 17.467 0.00 0.00 N1
> H
> END
>
>
> sorry if the text is too long .
>
> Raghav
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:28 CST