VMD-L Mailing List

From: Sasha Perkins (slp300_at_psu.edu)
Date: Thu Nov 08 2012 - 16:40:39 CST

Hello,

This may be a trivial question, however, I'm stuck on why the psf file that
psfgen creates, has dihedrals with the two atoms with the same number (i.e.
1 2 6 2, among others in my psf file). Shouldn't each dihedral listed in
the psf file be unique for every for atoms? Below is my psf file generated
by psfgen. Following that is a section of the topology file pertaining to
this residue.

*my psf file:*

PSF

       3 !NTITLE
 REMARKS original generated structure charmm psf file
 REMARKS topology top_all22_DES.inp
 REMARKS segment U { first NONE; last NONE; auto angles dihedrals }

      21 !NATOM
       1 U 1 CHO N3 123 0.581800 14.0070 0
       2 U 1 CHO C5 124 -0.229700 12.0110 0
       3 U 1 CHO C2 125 -0.395000 12.0110 0
       4 U 1 CHO C3 125 -0.395000 12.0110 0
       5 U 1 CHO C4 125 -0.395000 12.0110 0
       6 U 1 CHO H51 126 0.125900 1.0080 0
       7 U 1 CHO H52 126 0.125900 1.0080 0
       8 U 1 CHO H21 126 0.161300 1.0080 0
       9 U 1 CHO H22 126 0.161300 1.0080 0
      10 U 1 CHO H23 126 0.161300 1.0080 0
      11 U 1 CHO H31 126 0.161300 1.0080 0
      12 U 1 CHO H32 126 0.161300 1.0080 0
      13 U 1 CHO H33 126 0.161300 1.0080 0
      14 U 1 CHO H41 126 0.161300 1.0080 0
      15 U 1 CHO H42 126 0.161300 1.0080 0
      16 U 1 CHO H43 126 0.161300 1.0080 0
      17 U 1 CHO C6 124 0.396600 12.0110 0
      18 U 1 CHO H61 122 0.005700 1.0080 0
      19 U 1 CHO H62 122 0.005700 1.0080 0
      20 U 1 CHO OH1 127 -0.812600 15.9990 0
      21 U 1 CHO HO1 128 0.503700 1.0080 0

      22 !NBOND: bonds
       1 2 1 3 1 4 1 5
       2 6 2 7 2 17 2 6
       2 7 3 8 3 9 3 10
       4 11 4 12 4 13 5 14
       5 15 5 16 17 18 17 19
      17 20 20 21

      48 !NTHETA: angles
       1 5 16 1 5 15 1 5 14
       1 4 13 1 4 12 1 4 11
       1 3 10 1 3 9 1 3 8
       1 2 7 1 2 6 1 2 17
       1 2 7 1 2 6 2 17 20
       2 17 19 2 17 18 2 7 2
       2 6 2 2 1 5 2 1 4
       2 1 3 3 1 5 3 1 4
       4 1 5 6 2 7 6 2 7
       6 2 6 6 2 17 6 2 7
       7 2 7 7 2 6 7 2 17
       8 3 10 8 3 9 9 3 10
      11 4 13 11 4 12 12 4 13
      14 5 16 14 5 15 15 5 16
      17 20 21 17 2 7 17 2 6
      18 17 20 18 17 19 19 17 20

      78 !NPHI: dihedrals
       1 2 6 2 1 2 7 2
       1 2 17 18 1 2 17 19
       1 2 17 20 1 2 6 2
       1 2 7 2 2 17 20 21
       2 7 2 6 2 7 2 6
       2 7 2 17 2 7 2 6
       2 7 2 7 2 7 2 17
       2 7 2 6 2 6 2 7
       2 6 2 17 2 6 2 6
       2 6 2 7 2 6 2 7
       2 6 2 17 2 6 2 7
       2 1 3 8 2 1 3 9
       2 1 3 10 2 1 4 11
       2 1 4 12 2 1 4 13
       2 1 5 14 2 1 5 15
       2 1 5 16 3 1 2 6
       3 1 2 7 3 1 2 17
       3 1 2 6 3 1 2 7
       3 1 4 11 3 1 4 12
       3 1 4 13 3 1 5 14
       3 1 5 15 3 1 5 16
       4 1 2 6 4 1 2 7
       4 1 2 17 4 1 2 6
       4 1 2 7 4 1 3 8
       4 1 3 9 4 1 3 10
       4 1 5 14 4 1 5 15
       4 1 5 16 5 1 2 6
       5 1 2 7 5 1 2 17
       5 1 2 6 5 1 2 7
       5 1 3 8 5 1 3 9
       5 1 3 10 5 1 4 11
       5 1 4 12 5 1 4 13
       6 2 17 18 6 2 17 19
       6 2 17 20 6 2 17 18
       6 2 17 19 6 2 17 20
       7 2 17 18 7 2 17 19
       7 2 17 20 7 2 17 18
       7 2 17 19 7 2 17 20
      18 17 20 21 19 17 20 21

       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

       1 0 !NGRP
       0 0 0

*A section of the topology file I'm using:*
*
*
MASS 122 HAL2 1.00800 H !
MASS 123 NTL 14.00700 N !
MASS 124 CTL2 12.01100 C !
MASS 125 CTL5 12.01100 C !
MASS 126 HL 1.00800 H !
MASS 127 OHL 15.99900 O !
MASS 128 HOL 1.00800 H !

DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
AUTO ANGLES DIHE

RESI CHO 1.00 !
GROUP !
ATOM N3 NTL 0.5818 !
ATOM C5 CTL2 -0.2297 !
ATOM C2 CTL5 -0.3950 !
ATOM C3 CTL5 -0.3950 !
ATOM C4 CTL5 -0.3950 !
ATOM H51 HL 0.1259 !
ATOM H52 HL 0.1259 !
ATOM H21 HL 0.1613 !
ATOM H22 HL 0.1613 !
ATOM H23 HL 0.1613 !
ATOM H31 HL 0.1613 !
ATOM H32 HL 0.1613 !
ATOM H33 HL 0.1613 !
ATOM H41 HL 0.1613 !
ATOM H42 HL 0.1613 !
ATOM H43 HL 0.1613 !
ATOM C6 CTL2 0.3966 !
ATOM H61 HAL2 0.0057 !
ATOM H62 HAL2 0.0057 !
ATOM OH1 OHL -0.8126 !
ATOM HO1 HOL 0.5037 !
BOND N3 C5 N3 C2 N3 C3 N3 C4
BOND C5 H51 C5 H52 C5 C6
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND C6 H61 C6 H62
BOND C6 OH1 OH1 HO1
ACCE OH1 C2 C3 C4 C5 C6
DONOR HO1 OH1
DONOR HAL2 CTL2
DONOR HL CTL5
IC C4 N3 C5 C6 1.4964 107.76 161.60 116.58 1.5208
IC C6 C5 N3 C2 1.5208 116.58 -80.13 111.04 1.5031
IC C6 C5 N3 C3 1.5208 116.58 42.05 111.71 1.4945
IC N3 C5 C6 OH1 1.5158 116.58 56.02 109.57 1.3947
IC C5 C6 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491
IC C2 N3 C5 H51 1.5031 111.04 158.76 106.72 1.0813
IC C3 N3 C5 H52 1.4945 111.71 165.25 106.14 1.0802
IC C5 N3 C2 H21 1.5158 111.04 -179.38 108.21 1.0796
IC C3 N3 C2 H22 1.4945 109.20 -63.85 109.22 1.0746
IC C4 N3 C2 H23 1.4964 108.15 57.69 108.56 1.0794
IC C5 N3 C3 H31 1.5158 111.71 173.42 108.53 1.0794
IC C2 N3 C3 H32 1.5031 109.20 177.22 109.23 1.0800
IC C4 N3 C3 H33 1.4964 108.88 174.14 109.12 1.0773
IC C5 N3 C4 H41 1.5158 107.76 175.04 109.01 1.0793
IC C2 N3 C4 H42 1.5031 108.15 -64.86 109.05 1.0796
IC C3 N3 C4 H43 1.4945 108.88 56.40 109.30 1.0794
IC N3 C5 C6 H61 1.5158 116.58 176.61 105.66 1.0855

I may be missing something, any help would be greatly appreciated!

Thanks,

Sasha Perkins
Penn State University MatSE graduate student