Dear Jim,
By "mol" file format do you mean "mol2" file format ?
This file format is rigorously defined .
http://tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
Many programs generate their own "version" of this format with small
adaptations which are more or less correct//more or less understood by
others programs...
LEaP does recognize a well defined mol2 file format.
See basic examples of correct mol2 file format recognized by LEaP in
R.E.DD.B.:
http://q4md-forcefieldtools.org/REDDB/Projects/W-1/tripos1.mol2
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/tripos1.mol2
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/tripos2.mol2
...
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/tripos10.mol2
regards, Francois
> I converted a pdf file to mol file with Gaussian Viewer.
> I used xleap to load but it can not work.
>
> this is the e.g. of my mol file converted from Gaussian.
> ------------------------------------------------------
>
> .<TRIPOS>MOLECULE
> Molecule Name
> 35 36
> SMALL
> NO_CHARGES
>
>
> .<TRIPOS>ATOM
> 1 C1 0.8518 1.6927 0.2916 C
> 2 H2 -0.0122 2.0457 0.8186 H
> .......
> ------------------------------------------------------------
>
> if i changed the Gaussian file as the following. xleap works:
> -----------------------------------------------------------
> ......
> .<TRIPOS>MOLECULE
> *SUS*
> 35 36
> SMALL
> NO_CHARGES
>
>
> .<TRIPOS>ATOM
> 1 C1 0.8518 1.6927 0.2916 C *1 SUS 0*
> 2 H2 -0.0122 2.0457 0.8186 H *1 SUS 0*
>
> .....
> --------------------------------------------------------------------
> Can anyone help explain the meaning of the format of mol for xleap?
> what is meaning of 1 SUS 0 after the x, y, z coordinates? i know the last
> one is for partial charge
> what is the meaning of first two ones.
> i am new to amber
> thanks.
>
> Jim
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Received on Thu Jan 28 2010 - 20:00:02 PST
