VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 11 2011 - 00:14:01 CDT
- Next message: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Previous message: Marc Charendoff: "Molefacture - VMD agreement"
- In reply to: Marc Charendoff: "Molefacture - VMD agreement"
- Next in thread: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Reply: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Thu, Aug 11, 2011 at 12:10 AM, Marc Charendoff
<mcharend_at_sbcglobal.net> wrote:
> Hello,
> I am trying to create the hydrolysis product of a lactone ring in
> Molefacture from an existing structure so as to show the resulting alcohol
> and carboxylate functional groups. Everything looks ok in Molefacture, but
> when I write the resulting pdb file and reopen it in VMD I still see that
> the old carbonyl carbon to ether oxygen linkage remains. What am I missing?
a pdb file (as written by VMD) contains no information about bonding
and this is recovered heuristically from atom radii and distances on
loading the file. if you save a .pdb _and_ .psf file and then load the
.psf file with the .pdb file, then the bonding pattern will be read from
the psf. file rather than guessed heuristically.
there are also some other file formats that store bond information
alongside the coordinate information.
axel.
> Any guidance anyone could provide would be greatly appreciated. My current
> (failed structure) is below:
> REMARK original generated coordinate pdb file
> HETATM 1 OAO UNK B 253 29.310 34.583 39.046 1.00 0.00 MOL
> O
> HETATM 2 CAN UNK B 253 28.739 33.746 38.365 1.00 0.00 MOL
> C
> HETATM 3 OAR UNK B 253 28.383 33.934 37.053 1.00 0.00 MOL
> O
> HETATM 4 CAP UNK B 253 29.367 32.494 36.772 1.00 0.00 MOL
> C
> HETATM 5 CAQ UNK B 253 28.673 31.448 37.720 1.00 0.00 MOL
> C
> HETATM 6 CAM UNK B 253 28.249 32.381 38.825 1.00 0.00 MOL
> C
> HETATM 7 NAK UNK B 253 27.290 32.448 39.923 1.00 0.00 MOL
> N
> HETATM 8 HA2 UNK B 253 26.388 32.836 39.732 1.00 0.00 MOL
> H
> HETATM 9 CAJ UNK B 253 27.531 32.036 41.135 1.00 0.00 MOL
> C
> HETATM 10 OAL UNK B 253 28.345 31.134 41.344 1.00 0.00 MOL
> O
> HETATM 11 CAI UNK B 253 26.766 32.648 42.312 1.00 0.00 MOL
> C
> HETATM 12 CAH UNK B 253 25.626 33.644 42.084 1.00 0.00 MOL
> C
> HETATM 13 CAG UNK B 253 25.773 35.117 41.669 1.00 0.00 MOL
> C
> HETATM 14 CAF UNK B 253 24.963 36.102 42.502 1.00 0.00 MOL
> C
> HETATM 15 CAE UNK B 253 25.869 36.510 43.652 1.00 0.00 MOL
> C
> HETATM 16 CAD UNK B 253 25.128 37.706 44.254 1.00 0.00 MOL
> C
> HETATM 17 CAC UNK B 253 24.353 37.255 45.496 1.00 0.00 MOL
> C
> HETATM 18 CAB UNK B 253 25.083 36.081 46.154 1.00 0.00 MOL
> C
> HETATM 19 CAA UNK B 253 24.070 35.189 46.874 1.00 0.00 MOL
> C
> HETATM 20 CAS UNK B 253 23.084 34.560 45.886 1.00 0.00 MOL
> C
> HETATM 21 CAT UNK B 253 23.849 33.685 44.890 1.00 0.00 MOL
> C
> HETATM 22 OAM UNK B 253 29.738 32.082 35.940 1.00 0.00 MOL
> O
> END
> The desired product (w/regards to the opened lactone ring) is as follows:
>
> HETATM 2104 O4 C6L A 253 -15.207 -7.751 15.430 0.90 20.62
> O
>
> HETATM 2105 C5 C6L A 253 -16.064 -6.960 15.205 0.90 21.63
> C
>
> HETATM 2106 C6 C6L A 253 -16.833 -6.344 16.384 0.90 24.08
> C
>
> HETATM 2107 C7 C6L A 253 -17.971 -5.350 16.157 0.90 29.16
> C
>
> HETATM 2108 C8 C6L A 253 -17.824 -3.877 15.742 0.90 31.82
> C
>
> HETATM 2109 C9 C6L A 253 -18.634 -2.892 16.575 0.90 30.57
> C
>
> HETATM 2110 C10 C6L A 253 -17.724 -2.483 17.730 0.90 30.72
> C
>
> HETATM 2111 N1 C6L A 253 -16.307 -6.546 13.996 0.90 21.59
> N
>
> HETATM 2112 C3 C6L A 253 -15.573 -6.989 12.814 0.90 21.15
> C
>
> HETATM 2113 C4 C6L A 253 -14.550 -5.958 12.306 0.90 21.16
> C
>
> HETATM 2114 O2 C6L A 253 -14.258 -5.884 11.135 0.90 19.59
> O
>
> HETATM 2115 O1 C6L A 253 -13.945 -5.227 13.080 0.90 17.44
> O
>
> HETATM 2116 C2 C6L A 253 -16.571 -7.274 11.693 0.90 22.47
> C
>
> HETATM 2117 C1 C6L A 253 -16.106 -8.309 10.659 0.90 22.14
> C
>
> HETATM 2118 O3 C6L A 253 -15.111 -7.792 9.768 0.90 20.66
> O
>
> END
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
- Next message: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Previous message: Marc Charendoff: "Molefacture - VMD agreement"
- In reply to: Marc Charendoff: "Molefacture - VMD agreement"
- Next in thread: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Reply: Jernej Zidar: "Re: Molefacture - VMD agreement"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]