Dear All,
1) (using Firefox 45.0 for Ubuntu)
- When we use the jmol-14.4.3_2016.03.02 version - ('legacy' i.e. we
use Jmol.js) - See:
http://q4md-forcefieldtools.org/REDServer-Development/mol2-Jmol/javaapplet1111a.html
which displays the following mol2 file:
http://q4md-forcefieldtools.org/REDServer-Development/mol2-Jmol/tripos1.mol2
[...]
<script type='text/javascript'
src='../../jmol-14.4.3_2016.03.02-legacy/Jmol.js'></script>
[...]
<br /><br /><script
type='text/javascript'>jmolInitialize('../../jmol-14.4.3_2016.03.02-legacy',
true);</script>
[...]
jmolApplet(350, 'load ./tripos1.mol2; [...]
one can see, that some atoms are displayed in pink color with 'small
balls', meaning (I guess) that they are not 'well' recognized...
- When using jmol-12.1.15 - (we obviously use Jmol.js) - See:
http://q4md-forcefieldtools.org/REDServer-Development/mol2-Jmol/javaapplet1111b.html
which displays the same mol2 file
[...]
<script type='text/javascript' src='../../jmol-12.1.15/Jmol.js'></script>
[...]
<br /><br /><script
type='text/javascript'>jmolInitialize('../../jmol-12.1.15',
true);</script>
[...]
jmolApplet(350, 'load ./tripos1.mol2; [...]
one can see, that all the atoms are printed normally...
Why jmol-14.4.3_2016.03.02 does not 'correctly' recognize the atoms in
the tripos1.mol2 file, while jmol-12.1.15 does?
Is it because of the force field atom types, which are used in that
file? Indeed these atom types are NOT these of the Tripos force field,
but these of the Amber (Cornell et al.) force field. It is a general
strategy in AMBER to the use the Tripos file format for force field
libraries (so Amber force field atom types are printed in this file
type): thus the Tripos mol2 file format is not only used for the
Tripos force field...
2) We developed the mol3 file format, which derives from the that mol2
file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
The main difference is the appearance of a new column (the 10th) in
the 'mol2' file format in the '@<TRIPOS>ATOM' section
@<TRIPOS>ATOM
1 FE 0.461466 0.004161 -0.103993 FE 1 F01 3.0000 0.0000 ****
2 C1 2.293058 -2.492593 -0.144246 CC 1 F01 0.4252 0.3600 ****
[...]
This new column reports polarizabilities, which are used in the
non-additive (polarizable) Amber force field model:
is it possible, that Jmol recognizes this mol3 file format with
polarizability values as a new label?
thank you,
regards, Francois
F.-Y. Dupradeau
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