Re: Histamine topology file

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 12 2009 - 13:52:12 CDT

Hi,
the atom names in your pdb must correspond to the atom *names* (not
types) in the topology file, or else psgen cannot match up the
coordinates with the appropriate atoms.
Best,
Peter

r charbel maroun wrote:
> Hello,
>
> I've added a histamine residue to the top_all27_prot_lipid_na.inp CHARMM
> topology file. I created histamine from lysine's amino group and from
> histidine:
>
> RESI HME 0.00 ! neutral Histamine, proton on NE2, C Maroun 06/2009
> GROUP
> ATOM CE CT2 0.21
> ATOM HE3 HA 0.05
> ATOM HE4 HA 0.05
> ATOM NZ NH3 -0.30
> ATOM HZ1 HC 0.33
> ATOM HZ2 HC 0.33
> ATOM HZ3 HC 0.33
> GROUP ! HE1
> ATOM CB CT2 -0.08 ! __ /
> ATOM HB1 HA 0.09 ! HZ1 HE1 HB1 ND1--CE1
> ATOM HB2 HA 0.09 ! \ | | / |
> ATOM ND1 NR2 -0.70 !HZ2--NZ--CE--CB--CG |
> ATOM CG CPH1 0.22 ! / | | \\ |
> ATOM CE1 CPH2 0.25 ! HZ3 HE2 HB2 CD2--NE2
> ATOM HE1 HR1 0.13 ! | \
> GROUP ! HD2 HE2
> ATOM NE2 NR1 -0.36
> ATOM HE2 H 0.32
> ATOM CD2 CPH1 -0.05
> ATOM HD2 HR3 0.09
>
> BOND CG CB ND1 CG CE CB NZ CE
> BOND NE2 CD2 CE HE3 CE HE4
> BOND NE2 CE1 CB HB1
> BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
> DOUBLE CD2 CG CE1 ND1
> BOND NZ HZ1 NZ HZ2 NZ HZ3
> IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
> IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
> DONOR HZ1 NZ
> DONOR HZ2 NZ
> DONOR HZ3 NZ
> DONOR HE2 NE2
> ACCEPTOR ND1
> IC CG CE *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
> IC CG CE *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
> IC CE CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
> IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
> IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
> IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
> IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
> IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996
> IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809
> IC CG CB CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604
> IC NZ CB *CE HE3 1.4604 110.4600 119.9100 110.5100 1.1128
> IC NZ CB *CE HE4 1.4604 110.4600 -120.0200 110.5700 1.1123
> IC CB CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404
> IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402
> IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401
> PATCHING FIRST NONE LAST NONE
>
> The corresponding vmd pdb file is:
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 N HME A 1 1.152 -0.518 4.393 0.00
> 0.00 N
> ATOM 2 C HME A 1 0.086 -1.316 4.248 0.00
> 0.00 C
> ATOM 3 N HME A 1 -0.562 -1.013 3.110 0.00
> 0.00 N
> ATOM 4 C HME A 1 0.117 -0.009 2.526 0.00
> 0.00 C
> ATOM 5 C HME A 1 1.200 0.306 3.343 0.00
> 0.00 C
> ATOM 6 C HME A 1 -0.221 0.613 1.232 0.00
> 0.00 C
> ATOM 7 C HME A 1 0.482 -0.115 0.063 0.00
> 0.00 C
> ATOM 8 N HME A 1 0.154 0.519 -1.218 0.00
> 0.00 N
> ATOM 9 H HME A 1 1.784 -0.539 5.130 0.00
> 0.00 H
> ATOM 10 H HME A 1 -0.189 -2.050 4.902 0.00
> 0.00 H
> ATOM 11 H HME A 1 1.907 1.027 3.174 0.00
> 0.00 H
> ATOM 12 H HME A 1 0.077 1.665 1.240 0.00
> 0.00 H
> ATOM 13 H HME A 1 -1.303 0.571 1.085 0.00
> 0.00 H
> ATOM 14 H HME A 1 0.165 -1.161 0.019 0.00
> 0.00 H
> ATOM 15 H HME A 1 1.566 -0.080 0.193 0.00
> 0.00 H
> ATOM 16 H HME A 1 -0.857 0.483 -1.369 0.00
> 0.00 H
> ATOM 17 H HME A 1 0.463 1.493 -1.204 0.00
> 0.00 H
> ATOM 18 H HME A 1 0.628 0.023 -1.977 0.00
> 0.00 H
> END
>
> When I use AutoPSF to generate pdb and psf files for calculations, I get
> a (0,0,0) coordinates for all histamine atoms :
>
> REMARK original generated coordinate pdb file
> ATOM 1 CE HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 C
> ATOM 2 HE3 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 3 HE4 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 4 NZ HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 N
> ATOM 5 HZ1 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 6 HZ2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 7 HZ3 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 8 CB HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 C
> ATOM 9 HB1 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 10 HB2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 11 ND1 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 N
> ATOM 12 CG HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 C
> ATOM 13 CE1 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 C
> ATOM 14 HE1 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 15 NE2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 N
> ATOM 16 HE2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> ATOM 17 CD2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 C
> ATOM 18 HD2 HME X 0 0.000 0.000 0.000 -1.00 0.00
> O1 H
> END
>
>
> even though the psf file seems correct :
>
> PSF
>
> 3 !NTITLE
> REMARKS original generated structure x-plor psf file
> REMARKS topology HME_marvin_autopsf-temp.top
> REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
>
> 18 !NATOM
> 1 O1 0 HME CE CT2 0.210000 12.0110 0
> 2 O1 0 HME HE3 HA 0.050000 1.0080 0
> 3 O1 0 HME HE4 HA 0.050000 1.0080 0
> 4 O1 0 HME NZ NH3 -0.300000 14.0070 0
> 5 O1 0 HME HZ1 HC 0.330000 1.0080 0
> 6 O1 0 HME HZ2 HC 0.330000 1.0080 0
> 7 O1 0 HME HZ3 HC 0.330000 1.0080 0
> 8 O1 0 HME CB CT2 -0.080000 12.0110 0
> 9 O1 0 HME HB1 HA 0.090000 1.0080 0
> 10 O1 0 HME HB2 HA 0.090000 1.0080 0
> 11 O1 0 HME ND1 NR2 -0.700000 14.0070 0
> 12 O1 0 HME CG CPH1 0.220000 12.0110 0
> 13 O1 0 HME CE1 CPH2 0.250000 12.0110 0
> 14 O1 0 HME HE1 HR1 0.130000 1.0080 0
> 15 O1 0 HME NE2 NR1 -0.360000 14.0070 0
> 16 O1 0 HME HE2 H 0.320000 1.0080 0
> 17 O1 0 HME CD2 CPH1 -0.050000 12.0110 0
> 18 O1 0 HME HD2 HR3 0.090000 1.0080 0
>
> 18 !NBOND: bonds
> 1 8 1 2 1 3 4 1
> 4 5 4 6 4 7 8 9
> 8 10 11 12 12 8 13 14
> 13 11 15 17 15 13 15 16
> 17 18 17 12
>
> 31 !NTHETA: angles
> 1 8 10 1 8 9 1 4 7
> 1 4 6 1 4 5 2 1 3
> 4 1 3 4 1 2 5 4 7
> 5 4 6 6 4 7 8 12 17
> 8 12 11 8 1 3 8 1 2
> 8 1 4 9 8 10 11 12 17
> 12 11 13 12 8 10 12 8 9
> 12 8 1 13 15 16 14 13 11
> 15 17 12 15 17 18 15 13 11
> 15 13 14 17 15 16 17 15 13
> 18 17 12
>
> 40 !NPHI: dihedrals
> 1 8 12 11 1 8 12 17
> 2 1 8 12 2 1 8 9
> 2 1 8 10 2 1 4 5
> 2 1 4 6 2 1 4 7
> 3 1 8 12 3 1 8 9
> 3 1 8 10 3 1 4 5
> 3 1 4 6 3 1 4 7
> 4 1 8 12 4 1 8 9
> 4 1 8 10 5 4 1 8
> 6 4 1 8 7 4 1 8
> 8 12 11 13 8 12 17 15
> 8 12 17 18 9 8 12 11
> 9 8 12 17 10 8 12 11
> 10 8 12 17 11 13 15 17
> 11 13 15 16 11 12 17 15
> 11 12 17 18 12 17 15 13
> 12 17 15 16 12 11 13 15
> 12 11 13 14 13 15 17 18
> 13 11 12 17 14 13 15 17
> 14 13 15 16 16 15 17 18
>
> 6 !NIMPHI: impropers
> 13 11 15 14 13 15 11 14
> 15 17 13 16 15 13 17 16
> 17 12 15 18 17 15 12 18
>
> 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
>
> 1 0 !NGRP
> 0 0 0
>
> What could be going wrong ?
>
>
> Thanks in advance and nice weekend
>
> --
> R. Charbel MAROUN, PhD, HDR
> Neurobiologie et Pharmacologie
> MolÚculaire
> Centre de Psychiatrie et de
> Neurosciences Broca-Sainte Anne
> (INSERM U894)
> 2ter rue d'AlÚsia
> 75014 Paris
> FRANCE
> TÚl. +33 1 40 78 92 79
> Fax +33 1 45 80 72 93
> e-mail rmaroun_at_gmail.com <mailto:rmaroun_at_gmail.com>

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