On Tue, Jun 28, 2016, Martina Devi wrote:
>
> I gave the following command to convert mol2 file to prepin
>
> OAU=loadmol2 OAU.mol2
> saveamberprep OAU OAU.prep
>
> then I got the following lines:
>
> OAU: connect0 not defined
> OAU: connect1 not defined
mol2 files in Amber are intended primarily for ligands that are complete
molecules (and hence have no covalent connections to external atoms). The
mol3 format should be used if you wish to use a "mol2-like" format but
retain connection information that would be needed for things like modified
residues.
For more info:
http://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol3.php
...dac
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Received on Tue Jun 28 2016 - 10:30:02 PDT
