From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Sep 06 2013 - 08:55:42 CDT

Quoting Axel Kohlmeyer <akohlmey_at_gmail.com>:

thank you, regards, Francois

> 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