Dear Francois
Sorry, it should be mol2, not mol.
i am clear of the format now.
thanks for your information!
Jim
On Thu, Jan 28, 2010 at 7:43 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 22:30:03 PST
