From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 09 2012 - 04:12:47 CST

Check your topology. You have some bonds defined more than once.

On Nov 8, 2012, at 4:40 PM, Sasha Perkins wrote:

> 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