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From: _at_huji.ac.il
Date: Tue Jan 09 2007 - 10:06:25 CST

Dear NAMD and VMD users,
I'm trying to build topology file for sorbitol. I have used glycerol
topology file in order to do it. I'm using psfgen with this topology
file in order to create pdb and psf. The problem is that the molecule
created with this topology file is not sorbitol but its isomer. I have
tried to change the Internal coordinate definitions in topology file but
it looks like psfgen ignores this lines at all and creates the molecule
based on its own default parameters. The files i'm using are attached. I
hope somebody can help me with it.
Thank you in advance
Regina
The attached files:
sorbitol_alone.pdb - input file to psfgen in oder to create sorbitol
using only one coordinate (guesscoord can do it)
one_sorbitol.psf/pdb - output files from psfgen
topology file - sorbitol definitions at the end of file

PSF

       3 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS topology ../inp/top_all27_prot_lipid_ret_csff_adam_spc.rtf
 REMARKS segment SORB { first NONE; last NONE; auto angles dihedrals }

      26 !NATOM
       1 SORB 1 SORB C1 CTS 0.050000 12.0110 0
       2 SORB 1 SORB H11 HAS 0.100000 1.0080 0
       3 SORB 1 SORB H12 HAS 0.100000 1.0080 0
       4 SORB 1 SORB O1 OHS -0.650000 15.9994 0
       5 SORB 1 SORB H1 HOS 0.400000 1.0080 0
       6 SORB 1 SORB C2 CTS 0.150000 12.0110 0
       7 SORB 1 SORB H21 HAS 0.100000 1.0080 0
       8 SORB 1 SORB O2 OHS -0.650000 15.9994 0
       9 SORB 1 SORB H2 HOS 0.400000 1.0080 0
      10 SORB 1 SORB C3 CTS 0.150000 12.0110 0
      11 SORB 1 SORB H31 HAS 0.100000 1.0080 0
      12 SORB 1 SORB O3 OHS -0.650000 15.9994 0
      13 SORB 1 SORB H3 HOS 0.400000 1.0080 0
      14 SORB 1 SORB C4 CTS 0.150000 12.0110 0
      15 SORB 1 SORB H41 HAS 0.100000 1.0080 0
      16 SORB 1 SORB O4 OHS -0.650000 15.9994 0
      17 SORB 1 SORB H4 HOS 0.400000 1.0080 0
      18 SORB 1 SORB C5 CTS 0.150000 12.0110 0
      19 SORB 1 SORB H51 HAS 0.100000 1.0080 0
      20 SORB 1 SORB O5 OHS -0.650000 15.9994 0
      21 SORB 1 SORB H5 HOS 0.400000 1.0080 0
      22 SORB 1 SORB C6 CTS 0.050000 12.0110 0
      23 SORB 1 SORB H61 HAS 0.100000 1.0080 0
      24 SORB 1 SORB H62 HAS 0.100000 1.0080 0
      25 SORB 1 SORB O6 OHS -0.650000 15.9994 0
      26 SORB 1 SORB H6 HOS 0.400000 1.0080 0

      25 !NBOND: bonds
       1 2 1 3 1 4 1 6
       4 5 6 7 6 8 6 10
       8 9 10 11 10 12 10 14
      12 13 14 15 14 16 14 18
      16 17 18 19 18 20 18 22
      20 21 22 23 22 24 22 25
      25 26

      42 !NTHETA: angles
       1 6 10 1 6 8 1 6 7
       1 4 5 2 1 6 2 1 4
       2 1 3 3 1 6 3 1 4
       4 1 6 6 10 14 6 10 12
       6 10 11 6 8 9 7 6 10
       7 6 8 8 6 10 10 14 18
      10 14 16 10 14 15 10 12 13
      11 10 14 11 10 12 12 10 14
      14 18 22 14 18 20 14 18 19
      14 16 17 15 14 18 15 14 16
      16 14 18 18 22 25 18 22 24
      18 22 23 18 20 21 19 18 22
      19 18 20 20 18 22 22 25 26
      23 22 25 23 22 24 24 22 25

      63 !NPHI: dihedrals
       1 6 8 9 1 6 10 11
       1 6 10 12 1 6 10 14
       2 1 4 5 2 1 6 7
       2 1 6 8 2 1 6 10
       3 1 4 5 3 1 6 7
       3 1 6 8 3 1 6 10
       4 1 6 7 4 1 6 8
       4 1 6 10 5 4 1 6
       6 10 12 13 6 10 14 15
       6 10 14 16 6 10 14 18
       7 6 8 9 7 6 10 11
       7 6 10 12 7 6 10 14
       8 6 10 11 8 6 10 12
       8 6 10 14 9 8 6 10
      10 14 16 17 10 14 18 19
      10 14 18 20 10 14 18 22
      11 10 12 13 11 10 14 15
      11 10 14 16 11 10 14 18
      12 10 14 15 12 10 14 16
      12 10 14 18 13 12 10 14
      14 18 20 21 14 18 22 23
      14 18 22 24 14 18 22 25
      15 14 16 17 15 14 18 19
      15 14 18 20 15 14 18 22
      16 14 18 19 16 14 18 20
      16 14 18 22 17 16 14 18
      18 22 25 26 19 18 20 21
      19 18 22 23 19 18 22 24
      19 18 22 25 20 18 22 23
      20 18 22 24 20 18 22 25
      21 20 18 22 23 22 25 26
      24 22 25 26

       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

       1 0 !NGRP
       0 0 0