psfgen problem

From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Tue Jun 08 2004 - 04:53:39 CDT

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Hi All,

I am trying to read in a psf

% segment TEST {readpsf des.psf}
% coordpdb des.pdb TEST
building segment DES
reading structure from psf file des.psf
Info: generating structure...
Info: segment complete.
% coordpdb des.pdb TEST
reading coordinates from pdb
no residue 1 of segment TEST
Warning: failed to set coordinate for atom CP9
no residue 1 of segment TEST
Warning: failed to set coordinate for atom CP8

... and so on for every atom

The atomnames and residue name

Thanks in advance,

Marc

des.pdb:
ATOM 1 CP9 MOL 1
ATOM 2 CP8 MOL 1
ATOM 3 CP7 MOL 1
ATOM 4 CP6 MOL 1
ATOM 5 CP1 MOL 1
ATOM 6 CP2 MOL 1
ATOM 7 CP3 MOL 1
ATOM 8 OP3 MOL 1
ATOM 9 CP4 MOL 1
ATOM 10 CP5 MOL 1
ATOM 11 C7 MOL 1
ATOM 12 C6 MOL 1
ATOM 13 C5 MOL 1
ATOM 14 C4 MOL 1
ATOM 15 C3 MOL 1
ATOM 16 O3 MOL 1
ATOM 17 C2 MOL 1
ATOM 18 C1 MOL 1
ATOM 19 C8 MOL 1
ATOM 20 C9 MOL 1
ATOM 21 HP9 MOL 1
ATOM 22 HP9 MOL 1
ATOM 23 HP9 MOL 1
ATOM 24 HP8 MOL 1
ATOM 25 HP8 MOL 1
ATOM 26 HP1 MOL 1
ATOM 27 HP2 MOL 1
ATOM 28 HP3 MOL 1
ATOM 29 HP4 MOL 1
ATOM 30 HP5 MOL 1
ATOM 31 H5 MOL 1
ATOM 32 H4 MOL 1
ATOM 33 H3 MOL 1
ATOM 34 H2 MOL 1
ATOM 35 H1 MOL 1
ATOM 36 H81 MOL 1
ATOM 37 H82 MOL 1
ATOM 38 H91 MOL 1
ATOM 39 H92 MOL 1
ATOM 40 H93 MOL 1
TER 41 MOL 1
CONECT 1 2 21 22 23
CONECT 2 1 3 24 25
CONECT 3 2 4 11
CONECT 4 5 10 3
CONECT 5 6 4 26
CONECT 6 5 7 27
CONECT 7 6 8 9
CONECT 8 7 28
CONECT 9 7 10 29
CONECT 10 9 4 30
CONECT 11 3 12 19
CONECT 12 11 13 18
CONECT 13 12 14 31
CONECT 14 13 15 32
CONECT 15 14 16 17
CONECT 16 15 33
CONECT 17 15 18 34
CONECT 18 12 17 35
CONECT 19 11 20 36 37
CONECT 20 19 38 39 40
CONECT 21 1
CONECT 22 1
CONECT 23 1
CONECT 24 2
CONECT 25 2
CONECT 26 5
CONECT 27 6
CONECT 28 8
CONECT 29 9
CONECT 30 10
CONECT 31 13
CONECT 32 14
CONECT 33 16
CONECT 34 17
CONECT 35 18
CONECT 36 19
CONECT 37 19
CONECT 38 20
CONECT 39 20
CONECT 40 20
MASTER 3 0 0 0
END

des.psf:
PSF
       3
* File created by pdb2psf.sh
* (Script from Marc van der Kamp)
* DATE: Mon Jun 07 15:21:39 CEST 2004
     40 !NATOM
       1 MOL
       2 MOL
       3 MOL
       4 MOL
       5 MOL
       6 MOL
       7 MOL
       8 MOL
       9 MOL
      10 MOL 1
      11 MOL 1
      12 MOL 1
      13 MOL 1
      14 MOL 1
      15 MOL 1
      16 MOL 1
      17 MOL 1
      18 MOL 1
      19 MOL 1
      20 MOL 1
      21 MOL 1
      22 MOL 1
      23 MOL 1
      24 MOL 1
      25 MOL 1
      26 MOL 1
      27 MOL 1
      28 MOL 1
      29 MOL 1
      30 MOL 1
      31 MOL 1
      32 MOL 1
      33 MOL 1
      34 MOL 1
      35 MOL 1
      36 MOL 1
      37 MOL 1
      38 MOL 1
      39 MOL 1
      40 MOL 1
      41
       1
       2
       3
       5
       7
      10
      12
      14
      17
      19
      20
      68
       2
       1
      21
       3
       2
       3
       3
       4
       6
       7
       8
       7
      12
      11
      13
      12
      13
      14
      15
      18
      20
      19
      38
      94
      21
      21
      22
      23
      23
       1
      24
      25
       2
       2
      11
       4
       3
       3
       3
       3
      10
       5
       4
       4
      26
       5
      27
       6
       6
       8
       7
      19
      12
      12
      11
      11
      11
      18
      13
      12
      12
      31
      13
      32
      14
      14
      16
      15
      36
      36
      37
      14
       3
      11
      10
       7
      12
      18
      15
       2
       8
       2
       8
       0
       0
       0
       0
       0
       0
       1
       0

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This archive was generated by : Wed Feb 29 2012 - 15:38:43 CST and pdb file of a DES molecule in psfgen. This should be a simple procedure, however, when I read in the coordinates from the pdb-file after creating the segment with the psf-file, the coordinates can not be set because somehow the residue is not recongnized: file des.pdb for segment TEST MOL:1 TEST MOL:1 TEST and number are identical in my psf and pdb file (see below). The format of both files seems to be OK too (?) and reading in the psf and pdb file in VMD does work. So I don't know what causes the problem.... Can anybody help? 5.397 -3.084 -6.170 1.00 0.00 5.818 -2.066 -5.153 1.00 0.00 5.059 -0.745 -5.231 1.00 0.00 3.559 -0.898 -5.064 1.00 0.00 2.972 -0.997 -3.792 1.00 0.00 1.576 -1.171 -3.657 1.00 0.00 0.781 -1.244 -4.800 1.00 0.00 -0.587 -1.444 -4.729 1.00 0.00 1.351 -1.144 -6.071 1.00 0.00 2.729 -0.973 -6.185 1.00 0.00 5.633 0.426 -5.443 1.00 0.00 7.108 0.549 -5.815 1.00 0.00 7.536 0.304 -7.125 1.00 0.00 8.886 0.438 -7.482 1.00 0.00 9.819 0.817 -6.522 1.00 0.00 11.161 0.944 -6.829 1.00 0.00 9.422 1.069 -5.204 1.00 0.00 8.063 0.928 -4.868 1.00 0.00 4.899 1.768 -5.401 1.00 0.00 4.970 2.478 -4.072 1.00 0.00 5.952 -4.050 -6.113 1.00 0.00 5.464 -2.657 -7.198 1.00 0.00 4.322 -3.312 -5.980 1.00 0.00 6.917 -1.887 -5.214 1.00 0.00 5.613 -2.503 -4.148 1.00 0.00 3.606 -0.938 -2.891 1.00 0.00 1.119 -1.248 -2.656 1.00 0.00 -1.129 -1.494 -5.508 1.00 0.00 0.718 -1.200 -6.973 1.00 0.00 3.178 -0.895 -7.190 1.00 0.00 6.800 0.001 -7.889 1.00 0.00 9.206 0.244 -8.519 1.00 0.00 11.798 1.203 -6.174 1.00 0.00 10.160 1.372 -4.443 1.00 0.00 7.743 1.122 -3.830 1.00 0.00 3.837 1.640 -5.717 1.00 0.00 5.386 2.431 -6.153 1.00 0.00 4.435 3.456 -4.041 1.00 0.00 6.032 2.606 -3.756 1.00 0.00 4.483 1.815 -3.320 1.00 0.00 0 0 0 0 40 1 40 0 !NTITLE 1 MOL CP9 c3 -0.072859 12.0100 0 1 MOL CP8 c3 -0.043313 12.0100 0 1 MOL CP7 ce -0.041752 12.0100 0 1 MOL CP6 ca -0.029927 12.0100 0 1 MOL CP1 ca -0.070293 12.0100 0 1 MOL CP2 ca -0.051806 12.0100 0 1 MOL CP3 ca 0.049209 12.0100 0 1 MOL OP3 oh -0.409587 16.0000 0 1 MOL CP4 ca -0.051806 12.0100 0 MOL CP5 ca -0.070293 12.0100 0 MOL C7 cf -0.041752 12.0100 0 MOL C6 ca -0.029927 12.0100 0 MOL C5 ca -0.070293 12.0100 0 MOL C4 ca -0.051806 12.0100 0 MOL C3 ca 0.049209 12.0100 0 MOL O3 oh -0.409587 16.0000 0 MOL C2 ca -0.051806 12.0100 0 MOL C1 ca -0.070293 12.0100 0 MOL C8 c3 -0.043313 12.0100 0 MOL C9 c3 -0.072859 12.0100 0 MOL HP9 hc 0.027636 1.0080 0 MOL H6 hc 0.027636 1.0080 0 MOL H7 hc 0.027636 1.0080 0 MOL HP8 hc 0.039555 1.0080 0 MOL H10 hc 0.039555 1.0080 0 MOL HP1 ha 0.085236 1.0080 0 MOL HP2 ha 0.088215 1.0080 0 MOL HP3 ho 0.283505 1.0080 0 MOL HP4 ha 0.088215 1.0080 0 MOL HP5 ha 0.085236 1.0080 0 MOL H5 ha 0.085236 1.0080 0 MOL H4 ha 0.088215 1.0080 0 MOL H3 ho 0.283505 1.0080 0 MOL H2 ha 0.088215 1.0080 0 MOL H1 ha 0.085236 1.0080 0 MOL H81 hc 0.039555 1.0080 0 MOL H82 hc 0.039555 1.0080 0 MOL H91 hc 0.027636 1.0080 0 MOL H92 hc 0.027636 1.0080 0 MOL H93 hc 0.027636 1.0080 0 !NBOND: bonds 2 1 21 1 22 1 23 3 2 24 2 25 3 4 11 4 5 4 10 5 6 26 6 7 6 27 7 8 9 8 28 9 10 9 29 30 11 12 11 19 12 13 18 13 14 13 31 14 15 32 15 16 15 17 16 33 18 17 34 18 35 19 20 36 19 37 20 38 20 39 40 !NTHETA: angles 1 21 2 1 22 2 1 23 2 3 1 2 24 1 2 25 1 22 21 1 23 22 1 23 2 24 3 2 25 2 3 4 3 11 24 2 25 4 3 11 4 5 3 4 10 3 11 12 11 19 5 4 10 4 5 6 5 26 4 10 9 4 10 30 5 26 5 6 7 5 6 27 6 27 6 7 8 6 7 9 7 9 7 8 28 7 9 10 9 29 10 9 29 9 10 30 11 19 11 12 13 11 12 18 19 20 11 19 36 11 19 37 12 18 12 13 14 12 13 31 18 17 12 18 35 14 13 31 14 15 13 14 32 15 14 32 15 16 14 15 17 16 15 17 16 33 15 17 18 15 17 34 17 34 17 18 35 20 19 36 19 37 19 20 38 19 20 39 20 40 36 19 37 38 20 39 20 40 39 20 40 !NPHI: dihedrals 1 2 3 21 1 2 24 1 2 25 22 1 2 3 1 2 24 22 1 2 25 1 2 3 23 1 2 24 1 2 25 1 2 3 4 2 3 11 24 2 3 4 2 3 11 25 2 3 4 2 3 11 2 3 4 5 3 4 10 2 3 11 12 3 11 19 11 3 4 5 3 4 10 4 3 11 12 3 11 19 3 4 5 6 4 5 26 3 4 10 9 4 10 30 3 11 12 13 11 12 18 3 11 19 20 11 19 36 3 11 19 37 4 5 6 10 4 5 26 4 10 9 5 4 10 30 5 6 7 4 5 6 27 10 9 7 4 10 9 29 5 6 7 26 5 6 27 6 7 8 5 6 7 9 6 7 8 27 6 7 9 7 8 28 6 7 9 10 7 9 29 9 7 8 28 7 9 10 8 7 9 29 9 10 30 29 9 10 30 11 12 13 19 11 12 18 11 19 20 12 11 19 36 11 19 37 11 12 13 14 12 13 31 11 12 18 17 12 18 35 11 19 20 38 19 20 39 11 19 20 40 12 13 14 18 12 13 31 12 18 17 13 12 18 35 13 14 15 12 13 14 32 18 17 15 12 18 17 34 13 14 15 31 13 14 32 14 15 16 13 14 15 17 14 15 16 32 14 15 17 15 16 33 14 15 17 18 15 17 34 17 15 16 33 15 17 18 16 15 17 34 17 18 35 34 17 18 35 19 20 38 36 19 20 39 19 20 40 37 19 20 38 19 20 39 37 19 20 40 !NIMPHI: impropers 2 4 11 4 3 5 10 3 12 19 5 4 6 26 4 9 30 6 5 7 27 6 8 9 9 7 10 29 11 13 18 13 12 14 31 12 17 35 14 13 15 32 14 16 17 17 15 18 34 !NDON: donors 28 16 33 !NACC: acceptors 0 16 0 !NNB 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 !NGRP NST2 2 0 Brian Bennion: "Re: psfgen problem" Rad Balu: "Re: psfgen issue" Brian Bennion: "Re: psfgen problem" href="0661.html">Brian Bennion: "Re: psfgen problem" subject ] ] ] hypermail 2.1.6