[AMBER] using mol2 files with tleap

From: Jan Wahl <JanWahl.gmx.de>
Date: Thu, 09 Dec 2010 09:53:14 +0100

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 Universit├Ąt Frankfurt, Germany)
-- 
GMX DSL Doppel-Flat ab 19,99 &euro;/mtl.! Jetzt auch mit 
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Received on Thu Dec 09 2010 - 01:00:02 PST
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