Re: topology file for dissacharides with psfgen

From: Milton Sonoda (mtsonoda_at_gmail.com)
Date: Thu Apr 22 2010 - 00:11:03 CDT

Worked!! Now looks fine.
Thank you Mr. JC.

On Thu, Apr 22, 2010 at 1:46 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> Make sure to add “regenerate angles dihedrals” after you apply the patch.
>
>
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Milton Sonoda
> *Sent:* Wednesday, April 21, 2010 11:39 PM
> *To:* namd-l
> *Subject:* namd-l: topology file for dissacharides with psfgen
>
>
>
> 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
>

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

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