Dear Jan Wahl,
It looks like you do not have the force field atom types in the mol2
file but the chemical elements. Did you use R.E.D. or R.E.D. Server to
generate this mol2 file?
Before anything else you need to add the force field atom types.
- You could use LEaP for that.
See examples in R.E.DD.B. - for instance:
http://q4md-forcefieldtools.org/REDDB/project/W-46/
http://q4md-forcefieldtools.org/REDDB/project/W-46/script1.ff
- or you could use Antechamber to add force field atom types to the
mol2 file (and generate another mol2 file)
regards, Francois
> 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
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Received on Thu Dec 09 2010 - 03:00:02 PST
