topology file for dissacharides with psfgen

From: Milton Sonoda (mtsonoda_at_gmail.com)
Date: Wed Apr 21 2010 - 23:38:56 CDT

Dear all

I'm trying to construct a psf for a dissacharide, in this case trehalose,
file with psfgen.
In that order I'm employing the new MacKerell Charmm force field parameters
available at

http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_carbo_jan_2010.tgz

My psfgen run were fine. The psf, psfgen and pdb files are in the end of
this email.

The strange thing is in the psf file: although there is the record of the
O1-C1 bond
between the saccharides (atoms 2 and 24), there are no records of angles
and dihedrals involving atom 24 and other atoms of the first saccharide,
for instance, angle C1-O1-C1 (atoms 1, 2 and 24). This is odd since there
are these parameters in the parameter file.

The question is if it's that okay or there is really something wrong?

Milton Taidi Sonoda
Licenciatura em Física
Universidade Federal do Triângulo Mineiro - UFTM
Uberaba-MG
_______________________________________________________
PSF

       5 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 1 patches were applied to the molecule.
 REMARKS topology top_all36_carb_spce.rtf
 REMARKS segment TREH { first NONE; last NONE; auto angles dihedrals }
 REMARKS patch 11AA TREH:1 TREH:2

      45 !NATOM
       1 TREH 1 AGLC C1 CC3162 0.290000 12.0110 0
       2 TREH 1 AGLC O1 OC302 -0.360000 15.9994 0
       3 TREH 1 AGLC H1 HCA1 0.090000 1.0080 0
       4 TREH 1 AGLC C5 CC3163 0.110000 12.0110 0
       5 TREH 1 AGLC H5 HCA1 0.090000 1.0080 0
       6 TREH 1 AGLC O5 OC3C61 -0.400000 15.9994 0
       7 TREH 1 AGLC C2 CC3161 0.140000 12.0110 0
       8 TREH 1 AGLC H2 HCA1 0.090000 1.0080 0
       9 TREH 1 AGLC O2 OC311 -0.650000 15.9994 0
      10 TREH 1 AGLC HO2 HCP1 0.420000 1.0080 0
      11 TREH 1 AGLC C3 CC3161 0.140000 12.0110 0
      12 TREH 1 AGLC H3 HCA1 0.090000 1.0080 0
      13 TREH 1 AGLC O3 OC311 -0.650000 15.9994 0
      14 TREH 1 AGLC HO3 HCP1 0.420000 1.0080 0
      15 TREH 1 AGLC C4 CC3161 0.140000 12.0110 0
      16 TREH 1 AGLC H4 HCA1 0.090000 1.0080 0
      17 TREH 1 AGLC O4 OC311 -0.650000 15.9994 0
      18 TREH 1 AGLC HO4 HCP1 0.420000 1.0080 0
      19 TREH 1 AGLC C6 CC321 0.050000 12.0110 0
      20 TREH 1 AGLC H61 HCA2 0.090000 1.0080 0
      21 TREH 1 AGLC H62 HCA2 0.090000 1.0080 0
      22 TREH 1 AGLC O6 OC311 -0.650000 15.9994 0
      23 TREH 1 AGLC HO6 HCP1 0.420000 1.0080 0
      24 TREH 2 AGLC C1 CC3162 0.290000 12.0110 0
      25 TREH 2 AGLC H1 HCA1 0.090000 1.0080 0
      26 TREH 2 AGLC C5 CC3163 0.110000 12.0110 0
      27 TREH 2 AGLC H5 HCA1 0.090000 1.0080 0
      28 TREH 2 AGLC O5 OC3C61 -0.400000 15.9994 0
      29 TREH 2 AGLC C2 CC3161 0.140000 12.0110 0
      30 TREH 2 AGLC H2 HCA1 0.090000 1.0080 0
      31 TREH 2 AGLC O2 OC311 -0.650000 15.9994 0
      32 TREH 2 AGLC HO2 HCP1 0.420000 1.0080 0
      33 TREH 2 AGLC C3 CC3161 0.140000 12.0110 0
      34 TREH 2 AGLC H3 HCA1 0.090000 1.0080 0
      35 TREH 2 AGLC O3 OC311 -0.650000 15.9994 0
      36 TREH 2 AGLC HO3 HCP1 0.420000 1.0080 0
      37 TREH 2 AGLC C4 CC3161 0.140000 12.0110 0
      38 TREH 2 AGLC H4 HCA1 0.090000 1.0080 0
      39 TREH 2 AGLC O4 OC311 -0.650000 15.9994 0
      40 TREH 2 AGLC HO4 HCP1 0.420000 1.0080 0
      41 TREH 2 AGLC C6 CC321 0.050000 12.0110 0
      42 TREH 2 AGLC H61 HCA2 0.090000 1.0080 0
      43 TREH 2 AGLC H62 HCA2 0.090000 1.0080 0
      44 TREH 2 AGLC O6 OC311 -0.650000 15.9994 0
      45 TREH 2 AGLC HO6 HCP1 0.420000 1.0080 0

      46 !NBOND: bonds
       1 2 1 3 1 6 1 7
       2 24 4 5 4 19 4 6
       7 8 7 9 7 11 9 10
      11 12 11 13 11 15 13 14
      15 16 15 17 15 4 17 18
      19 20 19 21 19 22 22 23
      24 25 24 28 24 29 26 27
      26 41 26 28 29 30 29 31
      29 33 31 32 33 34 33 35
      33 37 35 36 37 38 37 39
      37 26 39 40 41 42 41 43
      41 44 44 45

      79 !NTHETA: angles
       1 7 11 1 7 9 1 7 8
       1 6 4 2 1 7 2 1 6
       2 1 3 3 1 7 3 1 6
       4 19 22 4 19 21 4 19 20
       5 4 6 5 4 19 6 1 7
       7 11 15 7 11 13 7 11 12
       7 9 10 8 7 11 8 7 9
       9 7 11 11 15 4 11 15 17
      11 15 16 11 13 14 12 11 15
      12 11 13 13 11 15 15 17 18
      15 4 6 15 4 19 15 4 5
      16 15 4 16 15 17 17 15 4
      19 22 23 19 4 6 20 19 22
      20 19 21 21 19 22 24 29 33
      24 29 31 24 29 30 24 28 26
      25 24 29 25 24 28 26 41 44
      26 41 43 26 41 42 27 26 28
      27 26 41 28 24 29 29 33 37
      29 33 35 29 33 34 29 31 32
      30 29 33 30 29 31 31 29 33
      33 37 26 33 37 39 33 37 38
      33 35 36 34 33 37 34 33 35
      35 33 37 37 39 40 37 26 28
      37 26 41 37 26 27 38 37 26
      38 37 39 39 37 26 41 44 45
      41 26 28 42 41 44 42 41 43
      43 41 44

     122 !NPHI: dihedrals
       1 7 9 10 1 7 11 12
       1 7 11 13 1 7 11 15
       1 6 4 15 1 6 4 5
       1 6 4 19 2 1 6 4
       2 1 7 8 2 1 7 9
       2 1 7 11 3 1 6 4
       3 1 7 8 3 1 7 9
       3 1 7 11 4 19 22 23
       4 15 11 7 4 15 11 12
       4 15 11 13 4 15 17 18
       4 6 1 7 5 4 15 11
       5 4 15 16 5 4 15 17
       5 4 19 20 5 4 19 21
       5 4 19 22 6 4 15 11
       6 4 15 16 6 4 15 17
       6 4 19 20 6 4 19 21
       6 4 19 22 6 1 7 8
       6 1 7 9 6 1 7 11
       7 11 13 14 7 11 15 16
       7 11 15 17 8 7 9 10
       8 7 11 12 8 7 11 13
       8 7 11 15 9 7 11 12
       9 7 11 13 9 7 11 15
      10 9 7 11 11 15 17 18
      11 15 4 19 12 11 13 14
      12 11 15 16 12 11 15 17
      13 11 15 16 13 11 15 17
      14 13 11 15 15 4 19 20
      15 4 19 21 15 4 19 22
      16 15 17 18 16 15 4 19
      17 15 4 19 20 19 22 23
      21 19 22 23 24 29 31 32
      24 29 33 34 24 29 33 35
      24 29 33 37 24 28 26 37
      24 28 26 27 24 28 26 41
      25 24 28 26 25 24 29 30
      25 24 29 31 25 24 29 33
      26 41 44 45 26 37 33 29
      26 37 33 34 26 37 33 35
      26 37 39 40 26 28 24 29
      27 26 37 33 27 26 37 38
      27 26 37 39 27 26 41 42
      27 26 41 43 27 26 41 44
      28 26 37 33 28 26 37 38
      28 26 37 39 28 26 41 42
      28 26 41 43 28 26 41 44
      28 24 29 30 28 24 29 31
      28 24 29 33 29 33 35 36
      29 33 37 38 29 33 37 39
      30 29 31 32 30 29 33 34
      30 29 33 35 30 29 33 37
      31 29 33 34 31 29 33 35
      31 29 33 37 32 31 29 33
      33 37 39 40 33 37 26 41
      34 33 35 36 34 33 37 38
      34 33 37 39 35 33 37 38
      35 33 37 39 36 35 33 37
      37 26 41 42 37 26 41 43
      37 26 41 44 38 37 39 40
      38 37 26 41 39 37 26 41
      42 41 44 45 43 41 44 45

       0 !NIMPHI: impropers

       0 !NDON: donors

       0 !NACC: acceptors

       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 0 0 0 0
       0 0 0 0 0

       1 0 !NGRP
       0 0 0

___________________________________________
topology top_all36_carb.rtf

pdbalias residue TRE AGLC ;

segment TREH {
 pdb trehalose.pdb
}

patch 11AA TREH:1 TREH:2

coordpdb trehalose.pdb TREH

guesscoord

writepsf out.psf
writepdb out.pdb

____________________________________________

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 TRE X 1 45.721 1.439 95.441 1.00 0.00
ATOM 2 O1 TRE X 1 45.359 0.160 95.873 1.00 0.00
ATOM 3 C5 TRE X 1 47.547 0.671 93.989 1.00 0.00
ATOM 4 O5 TRE X 1 47.167 1.539 95.076 1.00 0.00
ATOM 5 C2 TRE X 1 44.805 1.723 94.220 1.00 0.00
ATOM 6 O2 TRE X 1 43.483 1.588 94.642 1.00 0.00
ATOM 7 C3 TRE X 1 45.141 0.656 93.135 1.00 0.00
ATOM 8 O3 TRE X 1 44.332 0.873 92.023 1.00 0.00
ATOM 9 C4 TRE X 1 46.621 0.897 92.743 1.00 0.00
ATOM 10 O4 TRE X 1 47.054 -0.001 91.786 1.00 0.00
ATOM 11 C6 TRE X 1 49.015 0.902 93.760 1.00 0.00
ATOM 12 O6 TRE X 1 49.167 2.153 93.090 1.00 0.00
ATOM 13 C1 TRE X 2 45.982 -0.487 96.984 1.00 0.00
ATOM 14 C5 TRE X 2 44.589 0.573 98.723 1.00 0.00
ATOM 15 O5 TRE X 2 45.856 0.568 98.021 1.00 0.00
ATOM 16 C2 TRE X 2 45.932 -1.838 97.702 1.00 0.00
ATOM 17 O2 TRE X 2 46.047 -2.796 96.724 1.00 0.00
ATOM 18 C3 TRE X 2 44.477 -1.943 98.343 1.00 0.00
ATOM 19 O3 TRE X 2 44.339 -3.160 98.998 1.00 0.00
ATOM 20 C4 TRE X 2 44.425 -0.841 99.420 1.00 0.00
ATOM 21 O4 TRE X 2 43.174 -0.842 100.082 1.00 0.00
ATOM 22 C6 TRE X 2 44.585 1.696 99.744 1.00 0.00
ATOM 23 O6 TRE X 2 45.753 1.577 100.531 1.00 0.00
END 

-- 
Curso de Licenciatura em Física
Universidade Federal do Triângulo Mineiro - Uberaba
mtsonoda_at_gmail.com

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