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From: Dibyadeep Paul (dibyadeep_at_gmail.com)
Date: Wed Feb 13 2008 - 03:38:14 CST

Hii..

I am trying to use PSFGEN to generate the structure files for a structure,
using topology and pdb files generated by me. The topology and pdb files are
attached below. Since I generated the pdb file from scratch using tcl
scripts, I kept it to a minimum. The problem is that when I use the autopsf
facility to generate the psf file, I get the required psf file perfectly,
however when I use the following script :

package require psfgen
topology top_cnt.inp
segment U {pdb cnt3.pdb}
coordpdb cnt3.pdb U
writepdb cnt.pdb
writepsf cnt.psf

I get stuck at the segment command itself. On mannually running each of the
commands through the command line I got the following output:

building segment U
setting patch for first residue to NONE
setting patch for last residue to NONE
reading residues from pdb file cnt3.pdb
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
unknown residue type CNT
extracted 8 residues from pdb file
Info: generating structure...
unknown residue type CNT
*ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over*.

It seems psfgen is indeed recognising each residue, although it says of an
unknown residue, which I dont understand. I have defined the residue
properly in the topology file. Also why is it showing the errors and that
"MOLECULE DESTROYED BY FATAL ERROR!". The topology file is:

*> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
*>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
*>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
31 1
MASS 21 CA 12.01100 C ! aromatic C
AUTO ANGLES DIHE
RESI CNT 0.00 ! single loop of a C10 CNT
GROUP
ATOM C1 CA 0.00
ATOM C2 CA 0.00
ATOM C3 CA 0.00
ATOM C4 CA 0.00
ATOM C5 CA 0.00
ATOM C6 CA 0.00
ATOM C7 CA 0.00
ATOM C8 CA 0.00
ATOM C9 CA 0.00
ATOM C10 CA 0.00
ATOM C11 CA 0.00
ATOM C12 CA 0.00
ATOM C13 CA 0.00
ATOM C14 CA 0.00
ATOM C15 CA 0.00
ATOM C16 CA 0.00
ATOM C17 CA 0.00
ATOM C18 CA 0.00
ATOM C19 CA 0.00
ATOM C20 CA 0.00
BOND C1 C2 C2 C3 C3 C4 C4 C5
BOND C5 C6 C6 C7 C7 C8 C8 C9
BOND C9 C10 C10 C11 C11 C12
BOND C12 C13 C13 C14 C14 C15
BOND C15 C16 C16 C17 C17 C18
BOND C18 C19 C19 C20 C20 C1
BOND C2 +C1
BOND C4 +C3
BOND C6 +C5
BOND C8 +C7
BOND C10 +C9
BOND C12 +C11
BOND C14 +C13
BOND C16 +C15
BOND C18 +C17
BOND C20 +C19
PATCH FIRS NONE LAST NONE

and the pdb file:

ATOM 1 C1 CNT 1 -7.812 3.916 0.000
ATOM 2 C2 CNT 1 -7.101 3.724 1.210
ATOM 3 C3 CNT 1 -7.812 3.168 2.302
ATOM 4 C4 CNT 1 -7.101 2.302 3.168
ATOM 5 C5 CNT 1 -7.812 1.210 3.724
ATOM 6 C6 CNT 1 -7.101 0.000 3.916
ATOM 7 C7 CNT 1 -7.812 -1.210 3.724
ATOM 8 C8 CNT 1 -7.101 -2.302 3.168
ATOM 9 C9 CNT 1 -7.812 -3.168 2.302
ATOM 10 C10 CNT 1 -7.101 -3.724 1.210
ATOM 11 C11 CNT 1 -7.812 -3.916 0.000
ATOM 12 C12 CNT 1 -7.101 -3.724 -1.210
ATOM 13 C13 CNT 1 -7.812 -3.168 -2.302
ATOM 14 C14 CNT 1 -7.101 -2.302 -3.168
ATOM 15 C15 CNT 1 -7.812 -1.210 -3.724
ATOM 16 C16 CNT 1 -7.101 -0.000 -3.916
ATOM 17 C17 CNT 1 -7.812 1.210 -3.724
ATOM 18 C18 CNT 1 -7.101 2.302 -3.168
ATOM 19 C19 CNT 1 -7.812 3.168 -2.302
ATOM 20 C20 CNT 1 -7.101 3.724 -1.210
ATOM 21 C1 CNT 2 -5.681 3.724 1.210
ATOM 22 C2 CNT 2 -4.970 3.168 2.302
ATOM 23 C3 CNT 2 -5.681 2.302 3.168
ATOM 24 C4 CNT 2 -4.970 1.210 3.724
ATOM 25 C5 CNT 2 -5.681 0.000 3.916
ATOM 26 C6 CNT 2 -4.970 -1.210 3.724
ATOM 27 C7 CNT 2 -5.681 -2.302 3.168
ATOM 28 C8 CNT 2 -4.970 -3.168 2.302
ATOM 29 C9 CNT 2 -5.681 -3.724 1.210
ATOM 30 C10 CNT 2 -4.970 -3.916 0.000
ATOM 31 C11 CNT 2 -5.681 -3.724 -1.210
ATOM 32 C12 CNT 2 -4.970 -3.168 -2.302
ATOM 33 C13 CNT 2 -5.681 -2.302 -3.168
ATOM 34 C14 CNT 2 -4.970 -1.210 -3.724
ATOM 35 C15 CNT 2 -5.681 -0.000 -3.916
ATOM 36 C16 CNT 2 -4.970 1.210 -3.724
ATOM 37 C17 CNT 2 -5.681 2.302 -3.168
ATOM 38 C18 CNT 2 -4.970 3.168 -2.302
ATOM 39 C19 CNT 2 -5.681 3.724 -1.210
ATOM 40 C20 CNT 2 -4.970 3.916 -0.000
ATOM 41 C1 CNT 3 -3.550 3.168 2.302
ATOM 42 C2 CNT 3 -2.839 2.302 3.168
ATOM 43 C3 CNT 3 -3.550 1.210 3.724
ATOM 44 C4 CNT 3 -2.839 0.000 3.916
ATOM 45 C5 CNT 3 -3.550 -1.210 3.724
ATOM 46 C6 CNT 3 -2.839 -2.302 3.168
ATOM 47 C7 CNT 3 -3.550 -3.168 2.302
ATOM 48 C8 CNT 3 -2.839 -3.724 1.210
ATOM 49 C9 CNT 3 -3.550 -3.916 0.000
ATOM 50 C10 CNT 3 -2.839 -3.724 -1.210
ATOM 51 C11 CNT 3 -3.550 -3.168 -2.302
ATOM 52 C12 CNT 3 -2.839 -2.302 -3.168
ATOM 53 C13 CNT 3 -3.550 -1.210 -3.724
ATOM 54 C14 CNT 3 -2.839 -0.000 -3.916
ATOM 55 C15 CNT 3 -3.550 1.210 -3.724
ATOM 56 C16 CNT 3 -2.839 2.302 -3.168
ATOM 57 C17 CNT 3 -3.550 3.168 -2.302
ATOM 58 C18 CNT 3 -2.839 3.724 -1.210
ATOM 59 C19 CNT 3 -3.550 3.916 -0.000
ATOM 60 C20 CNT 3 -2.839 3.724 1.210
ATOM 61 C1 CNT 4 -1.419 2.302 3.168
ATOM 62 C2 CNT 4 -0.708 1.210 3.724
ATOM 63 C3 CNT 4 -1.419 0.000 3.916
ATOM 64 C4 CNT 4 -0.708 -1.210 3.724
ATOM 65 C5 CNT 4 -1.419 -2.302 3.168
ATOM 66 C6 CNT 4 -0.708 -3.168 2.302
ATOM 67 C7 CNT 4 -1.419 -3.724 1.210
ATOM 68 C8 CNT 4 -0.708 -3.916 0.000
ATOM 69 C9 CNT 4 -1.419 -3.724 -1.210
ATOM 70 C10 CNT 4 -0.708 -3.168 -2.302
ATOM 71 C11 CNT 4 -1.419 -2.302 -3.168
ATOM 72 C12 CNT 4 -0.708 -1.210 -3.724
ATOM 73 C13 CNT 4 -1.419 -0.000 -3.916
ATOM 74 C14 CNT 4 -0.708 1.210 -3.724
ATOM 75 C15 CNT 4 -1.419 2.302 -3.168
ATOM 76 C16 CNT 4 -0.708 3.168 -2.302
ATOM 77 C17 CNT 4 -1.419 3.724 -1.210
ATOM 78 C18 CNT 4 -0.708 3.916 -0.000
ATOM 79 C19 CNT 4 -1.419 3.724 1.210
ATOM 80 C20 CNT 4 -0.708 3.168 2.302
ATOM 81 C1 CNT 5 0.712 1.210 3.724
ATOM 82 C2 CNT 5 1.423 0.000 3.916
ATOM 83 C3 CNT 5 0.712 -1.210 3.724
ATOM 84 C4 CNT 5 1.423 -2.302 3.168
ATOM 85 C5 CNT 5 0.712 -3.168 2.302
ATOM 86 C6 CNT 5 1.423 -3.724 1.210
ATOM 87 C7 CNT 5 0.712 -3.916 0.000
ATOM 88 C8 CNT 5 1.423 -3.724 -1.210
ATOM 89 C9 CNT 5 0.712 -3.168 -2.302
ATOM 90 C10 CNT 5 1.423 -2.302 -3.168
ATOM 91 C11 CNT 5 0.712 -1.210 -3.724
ATOM 92 C12 CNT 5 1.423 -0.000 -3.916
ATOM 93 C13 CNT 5 0.712 1.210 -3.724
ATOM 94 C14 CNT 5 1.423 2.302 -3.168
ATOM 95 C15 CNT 5 0.712 3.168 -2.302
ATOM 96 C16 CNT 5 1.423 3.724 -1.210
ATOM 97 C17 CNT 5 0.712 3.916 -0.000
ATOM 98 C18 CNT 5 1.423 3.724 1.210
ATOM 99 C19 CNT 5 0.712 3.168 2.302
ATOM 100 C20 CNT 5 1.423 2.302 3.168
ATOM 101 C1 CNT 6 2.843 0.000 3.916
ATOM 102 C2 CNT 6 3.554 -1.210 3.724
ATOM 103 C3 CNT 6 2.843 -2.302 3.168
ATOM 104 C4 CNT 6 3.554 -3.168 2.302
ATOM 105 C5 CNT 6 2.843 -3.724 1.210
ATOM 106 C6 CNT 6 3.554 -3.916 0.000
ATOM 107 C7 CNT 6 2.843 -3.724 -1.210
ATOM 108 C8 CNT 6 3.554 -3.168 -2.302
ATOM 109 C9 CNT 6 2.843 -2.302 -3.168
ATOM 110 C10 CNT 6 3.554 -1.210 -3.724
ATOM 111 C11 CNT 6 2.843 -0.000 -3.916
ATOM 112 C12 CNT 6 3.554 1.210 -3.724
ATOM 113 C13 CNT 6 2.843 2.302 -3.168
ATOM 114 C14 CNT 6 3.554 3.168 -2.302
ATOM 115 C15 CNT 6 2.843 3.724 -1.210
ATOM 116 C16 CNT 6 3.554 3.916 -0.000
ATOM 117 C17 CNT 6 2.843 3.724 1.210
ATOM 118 C18 CNT 6 3.554 3.168 2.302
ATOM 119 C19 CNT 6 2.843 2.302 3.168
ATOM 120 C20 CNT 6 3.554 1.210 3.724
ATOM 121 C1 CNT 7 4.974 -1.210 3.724
ATOM 122 C2 CNT 7 5.685 -2.302 3.168
ATOM 123 C3 CNT 7 4.974 -3.168 2.302
ATOM 124 C4 CNT 7 5.685 -3.724 1.210
ATOM 125 C5 CNT 7 4.974 -3.916 0.000
ATOM 126 C6 CNT 7 5.685 -3.724 -1.210
ATOM 127 C7 CNT 7 4.974 -3.168 -2.302
ATOM 128 C8 CNT 7 5.685 -2.302 -3.168
ATOM 129 C9 CNT 7 4.974 -1.210 -3.724
ATOM 130 C10 CNT 7 5.685 -0.000 -3.916
ATOM 131 C11 CNT 7 4.974 1.210 -3.724
ATOM 132 C12 CNT 7 5.685 2.302 -3.168
ATOM 133 C13 CNT 7 4.974 3.168 -2.302
ATOM 134 C14 CNT 7 5.685 3.724 -1.210
ATOM 135 C15 CNT 7 4.974 3.916 -0.000
ATOM 136 C16 CNT 7 5.685 3.724 1.210
ATOM 137 C17 CNT 7 4.974 3.168 2.302
ATOM 138 C18 CNT 7 5.685 2.302 3.168
ATOM 139 C19 CNT 7 4.974 1.210 3.724
ATOM 140 C20 CNT 7 5.685 0.000 3.916
ATOM 141 C1 CNT 8 7.105 -2.302 3.168
ATOM 142 C2 CNT 8 7.816 -3.168 2.302
ATOM 143 C3 CNT 8 7.105 -3.724 1.210
ATOM 144 C4 CNT 8 7.816 -3.916 0.000
ATOM 145 C5 CNT 8 7.105 -3.724 -1.210
ATOM 146 C6 CNT 8 7.816 -3.168 -2.302
ATOM 147 C7 CNT 8 7.105 -2.302 -3.168
ATOM 148 C8 CNT 8 7.816 -1.210 -3.724
ATOM 149 C9 CNT 8 7.105 -0.000 -3.916
ATOM 150 C10 CNT 8 7.816 1.210 -3.724
ATOM 151 C11 CNT 8 7.105 2.302 -3.168
ATOM 152 C12 CNT 8 7.816 3.168 -2.302
ATOM 153 C13 CNT 8 7.105 3.724 -1.210
ATOM 154 C14 CNT 8 7.816 3.916 -0.000
ATOM 155 C15 CNT 8 7.105 3.724 1.210
ATOM 156 C16 CNT 8 7.816 3.168 2.302
ATOM 157 C17 CNT 8 7.105 2.302 3.168
ATOM 158 C18 CNT 8 7.816 1.210 3.724
ATOM 159 C19 CNT 8 7.105 0.000 3.916
ATOM 160 C20 CNT 8 7.816 -1.210 3.724
END

I would really appreciate any help you guys might provide. I have been
trying to understand why this problem is occuring for a long time now. I
actually have a much more complex problem at hand, but I want to understand
what I am doing wrong instead of using autopsf, so that when I try out the
larger problem, I dont do the mistakes then,which will be more difficult to
solve than this one.

Sincerely

DIbyadeep*
*