From: Soumyasaswati Sarangi (saswati_at_jncasr.ac.in)
Date: Tue Nov 07 2006 - 02:47:37 CST
Hi, I dont think anything is wrong in the output.
Why are you thinking so?
There may be some ring structures in your protein. so you are getting more
no of bonds than no of atoms.
Regards.
> I am an undergraduate researcher teaching myself computational
> chemistry. I am using top_all27_na.rtf as my forcefield. My initial
> structure is as follows
> ~~~
> ATOM 1 O5' THY 1 1.568 1.917 -0.000
> ATOM 63 H5T THY 1 0.996 1.758 -0.401
> ATOM 2 C5' THY 1 2.446 1.098 0.795
> ATOM 3 H5' THY 1 1.912 0.744 1.677
> ATOM 4 H5'' THY 1 2.777 0.247 0.201
> ATOM 5 C4' THY 1 3.660 1.905 1.228
> ATOM 6 H4' THY 1 4.126 1.428 2.090
> ATOM 7 O4' THY 1 4.672 1.834 0.178
> ATOM 8 C1' THY 1 4.728 3.065 -0.528
> ATOM 9 H1' THY 1 5.698 3.533 -0.365
> ATOM 10 N1 THY 1 4.600 2.800 -2.030
> ATOM 11 C6 THY 1 3.394 2.662 -2.664
> ATOM 12 H6 THY 1 2.476 2.738 -2.101
> ATOM 13 C5 THY 1 3.323 2.484 -3.990
> ATOM 14 C5M THY 1 2.007 2.331 -4.694
> ATOM 15 H51 THY 1 1.402 3.223 -4.532
> ATOM 16 H52 THY 1 2.179 2.198 -5.762
> ATOM 17 H53 THY 1 1.483 2.460 -4.300
> ATOM 18 C4 THY 1 4.518 2.433 -4.792
> ATOM 19 O4 THY 1 4.551 2.274 -6.011
> ATOM 20 N3 THY 1 5.805 2.476 -4.058
> ATOM 21 H3 THY 1 6.714 2.438 -4.659
> ATOM 22 C2 THY 1 5.793 2.712 -2.699
> ATOM 23 O2 THY 1 6.823 2.757 -2.046
> ATOM 24 C3' THY 1 3.425 3.404 1.430
> ATOM 25 H3' THY 1 2.451 3.546 1.899
> ATOM 26 C2' THY 1 3.625 3.971 0.023
> ATOM 27 H2' THY 1 2.711 4.465 -0.304
> ATOM 28 H2'' THY 1 4.443 4.691 0.034
> ATOM 29 O3' THY 1 4.330 4.077 2.292
> ATOM 30 P THY 1 4.481 5.665 2.173
> ATOM 31 O1P THY 1 4.720 6.243 3.514
> ATOM 32 O2P THY 1 3.326 6.219 1.431
> ATOM 33 O5' THY 1 5.807 5.792 1.287
> ATOM 34 C5' THY 1 6.897 4.882 1.526
> ATOM 35 H5' THY 1 6.912 4.603 2.580
> ATOM 36 H5'' THY 1 6.760 3.992 0.913
> ATOM 37 C4' THY 1 8.216 5.542 1.158
> ATOM 38 H4' THY 1 9.034 5.021 1.654
> ATOM 39 O4' THY 2 8.463 5.340 -0.266
> ATOM 40 C1' THY 2 8.233 6.549 -0.976
> ATOM 41 H1' THY 2 9.170 6.899 -1.410
> ATOM 42 N1 THY 2 7.269 6.287 -2.135
> ATOM 43 C6 THY 2 5.907 6.287 -1.989
> ATOM 44 H6 THY 2 5.468 6.478 -1.021
> ATOM 45 C5 THY 2 5.096 6.106 -3.040
> ATOM 46 C5M THY 2 3.603 6.105 -2.890
> ATOM 47 H51 THY 2 3.277 7.065 -2.489
> ATOM 48 H52 THY 2 3.140 5.943 -3.863
> ATOM 49 H53 THY 2 3.307 5.307 -2.209
> ATOM 50 C4 THY 2 5.634 5.905 -4.360
> ATOM 51 O4 THY 2 4.969 5.732 -5.381
> ATOM 52 N3 THY 2 7.109 5.801 -4.461
> ATOM 53 H3 THY 2 7.523 5.648 -5.458
> ATOM 54 C2 THY 2 7.875 6.050 -3.341
> ATOM 55 O2 THY 2 9.093 5.978 -3.369
> ATOM 56 C3' THY 2 8.275 7.060 1.344
> ATOM 57 H3' THY 2 7.744 7.322 2.259
> ATOM 58 C2' THY 2 7.713 7.585 0.021
> ATOM 59 H2' THY 2 6.822 8.182 0.216
> ATOM 60 H2'' THY 2 8.463 8.203 -0.473
> ATOM 61 O3' THY 2 9.565 7.628 1.513
> ATOM 62 H3T THY 2 10.116 7.733 2.071
> ATOM 64 SOD SOD 3 3.382 7.023 2.892
> CONECT 1 1 63
> CONECT 1 1 3 4 5
> CONECT 3 2
> CONECT 4 2
> CONECT 5 1 6 7 24
> CONECT 6 5
> CONECT 7 5 8
> CONECT 8 7 9 10 26
> CONECT 9 8
> CONECT 10 8 11 22
> CONECT 11 10 12 13
> CONECT 12 11
> CONECT 13 21 14 18
> CONECT 14 13 25 16 17
> CONECT 15 14
> CONECT 16 14
> CONECT 17 14
> CONECT 18 13 29 20
> CONECT 19 18
> CONECT 20 18 21 22
> CONECT 21 20
> CONECT 22 10 20 23
> CONECT 23 22
> CONECT 24 5 25 26 29
> CONECT 25 24
> CONECT 26 8 24 27 28
> CONECT 27 26
> CONECT 28 26
> CONECT 29 24 30
> CONECT 30 31 32 33 29
> CONECT 31 30
> CONECT 32 30
> CONECT 33 30 34
> CONECT 34 33 35 36 37
> CONECT 35 34
> CONECT 36 34
> CONECT 37 34 38 39 56
> CONECT 38 37
> CONECT 39 37 40
> CONECT 40 39 41 42 58
> CONECT 41 40
> CONECT 42 40 43 54
> CONECT 43 42 44 45
> CONECT 44 43
> CONECT 45 43 46 50
> CONECT 46 45 47 48 49
> CONECT 47 46
> CONECT 48 46
> CONECT 49 46
> CONECT 50 45 51 52
> CONECT 51 50
> CONECT 52 50 53 54
> CONECT 53 52
> CONECT 54 42 52 55
> CONECT 55 54
> CONECT 56 37 57 58 61
> CONECT 57 56
> CONECT 58 40 56 59 60
> CONECT 59 58
> CONECT 60 58
> CONECT 61 56 62
> CONECT 62 61
> CONECT 63 1
> END
> ~~~
>
> When I run the following script with VMD
> topology top_all27_na.rtf
> segment T {pdb TpT_B.ent}
> coordpdb TpT_B.ent T
> writepdb TpT.pdb
> writepsf TpT.psf
>
> The problem is the output from VMD is "total of 67 atoms
> total of 69 bonds
> total of 124 angles
> total of 179 dihedrals
> total of 6 impropers
> total of 0 cross-terms"
>
> Well, it seems the forcefield is not recognizing the H5T and H3T.
> Since I am new, is there anything I am missing? I just want to be
> able to run a MD simulation on this molecule using NAMD, but I can't
> get the proper topology or structure in the beginning.
>
> Thank you,
> Javad Azadi
> Undergraduate Researcher
> Kohler Group
> The Ohio State University
> jazadi_at_chemistry.osu.edu
> azadi.1_at_osu.edu
>
>
>
Soumya Saswati Sarangi
Ph.D Student
Molecular Simulations Lab.CPMU
JNCASR,Bangalore-560 064
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