Re: [Jmol-users] Atom color in .mol2 files

[Robert H. <ha...@st...>]

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 <fy...@q4...> 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