From: Javad Azadi (jazadi_at_chemistry.ohio-state.edu)
Date: Tue Nov 07 2006 - 12:12:49 CST
I did. It is 5TER and 3TER according to the forcefield, but it is ignored
by VMD and it builds a Thymine-Thymine structure even though I do not want
the phosphate group on the 3' end and I added the terminal hydrogens. Is
there a way to get the psf without this happening?
Thanks,
Javad
Richard Wood <rwoodphd_at_yahoo.com> said:
> Look in the topology for those atoms that correspond to H3T and H5T in
your pdb file and then change the names of H3T and H5T so that they are the
same as in the topology. This should help.
Richard
Richard L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030
rwoodphd_at_yahoo.com
----- Original Message ----
From: Javad Azadi <jazadi_at_chemistry.ohio-state.edu>
To: namd-l_at_ks.uiuc.edu
Sent: Tuesday, November 7, 2006 12:33:21 AM
Subject: namd-l: Trouble with Charmm/PDB?
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
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