VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 09 2007 - 11:11:04 CST

attached mail follows:

Hi Regina,
psfgen does indeed pay attention to internal coordinates, but you need
to give it more than one atom as a starting point or else it will just
need to guess. Try, for example, giving it C1/C2/C3, or all of the
carbons, and you'll see the effects of the IC lines (note that more
information is needed in the file you gave -- some bonds and angles
would be useful).

Peter

" politr"@huji.ac.il wrote:
> 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
>
>