H1 is not listed as an AMBER atom type in that reference I used. Nor H4 H5
HP
OK, so I've added those from the JACS paper.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Those pink H atoms should be gone.
Bob
On Thu, Oct 30, 2008 at 2:43 PM, FyD <[EMAIL PROTECTED]> wrote:
> Dear Bob,
>
> > This is done. Jmol 11.7.6 will display all mol2 atom types as found in
> the
> > file and map correctly (so I claim!) atom types to element symbols for
> the
> > following force fields:
> > AMBER, GAFF, ESFF, CFF91, CHARMM, COMPASS, CVFF, CVFF_aug, PCFF
>
> This is great... Thanks a lot !
>
> > as described in
> > http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html
>
> As you saw Accelrys Inc. uses the Tripos mol2 file format for their
> own FFs: CVFF, CFF etc... as people from AMBER.
>
> I started to use the version you provide @
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>
> A test is available @
> http://q4md-forcefieldtools.org/RED/index-test.php
>
> It looks like the hydrogens are pink:
> 1 C1 1.352237 -0.856933 0.225852 CT 1 DMSO -0.2897
> 2 H11 1.336243 -1.843530 -0.221408 H1 1 DMSO 0.1284
> 3 H12 1.276947 -0.923392 1.304085 H1 1 DMSO 0.1284
> 4 H13 2.275139 -0.356278 -0.035153 H1 1 DMSO 0.1284
> 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177
> 6 O3 -0.000040 1.405694 0.357557 O 1 DMSO -0.5085
> 7 C4 -1.352189 -0.857006 0.225851 CT 1 DMSO -0.2897
> 8 H41 -2.275117 -0.356396 -0.035149 H1 1 DMSO 0.1284
> 9 H42 -1.336143 -1.843599 -0.221415 H1 1 DMSO 0.1284
> 10 H43 -1.276895 -0.923466 1.304085 H1 1 DMSO 0.1284
>
> regards, Francois
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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