mol2 format - atom types and charge

Hi,

Following up from this topic and a few trials...

I haven't tried the splitting option (-m burried in the command line help - like the -F option, incidently) yet, but it will be useful.

The docking program I use has some problems with some atom types, though. For example, anisole. The atoms of the methoxy are declared as simply C and O atoms, when they should be declared as C.3 and O.3, and this gives a chain of behaviors:

• they are transformed in dummy atoms (atom type Du)


• the aromatic C.ar atom that bears the methoxy on the benzene ring also becomes a dummy atom by deduction


• the 2 other C.ar atoms attached to the latter then have suspicious valencies...

See the picture attached...

The USER_CHARGES are coming in version 5.2.3, right? I can't wait to use only chemaxon tools and not openbabel in conjonction ;-)

Cheers,

Nicolas

in case I'm not clear, the mol2 code below is generated by marvin and the C.ar are correctly defined, it is the docking program that messes up the declarations I showed before...

@<TRIPOS>MOLECULE
anisole
8 8
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 0.0000 4.6200 0.0000 C
2 O1 1.3337 3.8500 0.0000 O
3 C2 1.3337 2.3100 0.0000 C.ar
4 C3 2.6674 1.5400 0.0000 C.ar
5 C4 2.6674 -0.0000 0.0000 C.ar
6 C5 1.3337 -0.7700 0.0000 C.ar
7 C6 0.0000 0.0000 0.0000 C.ar
8 C7 0.0000 1.5400 0.0000 C.ar
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 ar
4 4 5 ar
5 5 6 ar
6 6 7 ar
7 7 8 ar
8 3 8 ar
@<TRIPOS>SUBSTRUCTURE
1 noname 1

 

 

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Hi Nicolas,

I'd like to confirm that charges will be available in 5.2.3. However, this feature will require a charge plugin license, apparently.

I'll get back later with a more detailed response regarding atom types.

bests

Miklos

 

 

Hi Miklos,

Thank you for the confirmation!

Cheers,

Nicolas