Re: [AMBER] using mol2 files with tleap

From: M. Shahid <mohammad.shahid.gmail.com>
Date: Thu, 9 Dec 2010 10:37:11 +0100

Hi,

first prepare the prep and frcmod file for your mol2 file by using
antechamber with a selected forcefield.
then load (with loadAmberPrep/loadAmberParm commands) those
prep/frcmodfiles in tleap before loading your mol2.

regards,

--
Shahid.
On Thu, Dec 9, 2010 at 9:53 AM, Jan Wahl <JanWahl.gmx.de> wrote:
> Hello community,
> i'm doing my first steps with amber 11. Therefore i have some trouble using
> tleap with mol2 files. my question is know, how should the input-file should
> look like to be accepted by tleap and saving a top and crd file. I always
> get this error
>
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - S
> Could not find bond parameter for: S - O
> Could not find bond parameter for: S - C
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - H
> Building angle parameters.
> Could not find angle parameter: C - S - O
> Could not find angle parameter: C - S - C
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - S
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - S
> Could not find angle parameter: H - C - S
> Could not find angle parameter: S - C - H
> Could not find angle parameter: S - C - H
> Could not find angle parameter: S - C - H
> Could not find angle parameter: O - S - C
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - H
> Building proper torsion parameters.
>  ** No torsion terms for  C-S-C-H
>  ** No torsion terms for  C-S-C-H
>  ** No torsion terms for  C-S-C-H
>  ** No torsion terms for  H-C-S-O
>  ** No torsion terms for  H-C-S-C
>  ** No torsion terms for  H-C-S-O
>  ** No torsion terms for  H-C-S-C
>  ** No torsion terms for  H-C-S-O
>  ** No torsion terms for  H-C-S-C
>  ** No torsion terms for  O-S-C-H
>  ** No torsion terms for  O-S-C-H
>  ** No torsion terms for  O-S-C-H
> Building improper torsion parameters.
>  total 0 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>
>
> i think the problem is a missing <unit> but the mol2 files was created
> using the program avogadro. is there a recommended programm for creating
> mol2 files which can be used with tleap?
>
>
>
> Thank you very much
>
>
> Jan Wahl
>
>
> (Goethe Universität Frankfurt, Germany)
> --
> GMX DSL Doppel-Flat ab 19,99 &euro;/mtl.! Jetzt auch mit
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>
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Received on Thu Dec 09 2010 - 02:00:03 PST