From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 06 2013 - 07:43:12 CDT

On Fri, Sep 6, 2013 at 1:35 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> Dear All,
>
> I use vmd 1.9.1 under Linux - version: 64 bits.
>
> Below two examples of pseudo .mol2 file:
>
> case -1: a single atom connectivity is defined within the hydroxyl group:
> only this bond is s displayed by vmd; no problem...
>
> case -2: no atom connectivity is defined within the entire molecule
> all bonds are displayed? Why?

because if a molecule reader plugin reports zero bonds *and* the
autobonds flag is set to 1 (which is the default), then VMD will guess
the bonds.

if you read the molecule with "autobonds 0", it should not generate any bonds.

"it's not a bug, it's a feature, man",
     axel.

> my understanding is that for the mol2 file format only reported bonds should
> be displayed.
>
> Thanks, regards, Francois
>
>
> case -1:
> @<TRIPOS>MOLECULE
> EOH
> 9 1 1 0 1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
> 1 CA1 1.172826 -0.410842 0.000000 C? 1 EOH -1.1742 0.0000 ****
> 2 HA11 2.122990 0.134817 0.000000 H? 1 EOH 0.4959 0.0000 ****
> 3 HA12 1.138127 -1.052076 0.886857 H? 1 EOH 0.4959 0.0000 ****
> 4 HA13 1.138127 -1.052076 -0.886857 H? 1 EOH 0.4959 0.0000 ****
> 5 CB1 0.000000 0.555645 0.000000 C? 1 EOH -1.1742 0.0000 ****
> 6 HB11 0.051209 1.207890 0.887543 H? 1 EOH 0.4959 0.0000 ****
> 7 HB12 0.051209 1.207890 -0.887543 H? 1 EOH 0.4959 0.0000 ****
> 8 O -1.198868 -0.214482 0.000000 O? 1 EOH -0.6270 0.0000 ****
> 9 HO -1.947675 0.400600 0.000000 H? 1 EOH 0.4959 0.0000 ****
> @<TRIPOS>BOND
> 1 8 9 1
> @<TRIPOS>SUBSTRUCTURE
> 1 EOH 1 **** 0 **** ****
> @<TRIPOS>HEADTAIL
> 0 0
> 0 0
> @<TRIPOS>RESIDUECONNECT
> 1 0 0 0 0 0 0
>
> -----------------------------------------------------------
>
> case -2:
> @<TRIPOS>MOLECULE
> EOH
> 9 0 1 0 1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
> 1 CA1 1.172826 -0.410842 0.000000 C? 1 EOH -1.1742 0.0000 ****
> 2 HA11 2.122990 0.134817 0.000000 H? 1 EOH 0.4959 0.0000 ****
> 3 HA12 1.138127 -1.052076 0.886857 H? 1 EOH 0.4959 0.0000 ****
> 4 HA13 1.138127 -1.052076 -0.886857 H? 1 EOH 0.4959 0.0000 ****
> 5 CB1 0.000000 0.555645 0.000000 C? 1 EOH -1.1742 0.0000 ****
> 6 HB11 0.051209 1.207890 0.887543 H? 1 EOH 0.4959 0.0000 ****
> 7 HB12 0.051209 1.207890 -0.887543 H? 1 EOH 0.4959 0.0000 ****
> 8 O -1.198868 -0.214482 0.000000 O? 1 EOH -0.6270 0.0000 ****
> 9 HO -1.947675 0.400600 0.000000 H? 1 EOH 0.4959 0.0000 ****
> @<TRIPOS>BOND
> @<TRIPOS>SUBSTRUCTURE
> 1 EOH 1 **** 0 **** ****
> @<TRIPOS>HEADTAIL
> 0 0
> 0 0
> @<TRIPOS>RESIDUECONNECT
> 1 0 0 0 0 0 0
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.