Histamine topology file

From: r charbel maroun (rmaroun_at_gmail.com)
Date: Fri Jun 12 2009 - 11:32:35 CDT

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

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