VMD-L Mailing List

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Sep 06 2013 - 06:35:52 CDT

• Next message: Subrata Paul: "water cluster size analysis"
• Previous message: Axel Kohlmeyer: "Re: Autobond Criterion"
• In reply to: Oliver Stenning: "Autobond Criterion"
• Next in thread: Axel Kohlmeyer: "Re: mol2 file format & displaying atom connectivities"
• Reply: Axel Kohlmeyer: "Re: mol2 file format & displaying atom connectivities"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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?
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

• Next message: Subrata Paul: "water cluster size analysis"
• Previous message: Axel Kohlmeyer: "Re: Autobond Criterion"
• In reply to: Oliver Stenning: "Autobond Criterion"
• Next in thread: Axel Kohlmeyer: "Re: mol2 file format & displaying atom connectivities"
• Reply: Axel Kohlmeyer: "Re: mol2 file format & displaying atom connectivities"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]