Hello,
On Tue, Mar 2, 2010 at 11:59 AM, N.R. Jena <nrjena.gmail.com> wrote:
> Thank you very much Prof. Case. There was no error message. It was like:
>
> {I am attaching herewith the .prepin and .frcmod files as well.}
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: OS - O2
> Could not find bond parameter for: CK - P
These are the error messages, same with the angle parameters and
dihedral parameters below them.
> Building angle parameters.
> Could not find angle parameter: OS - O2 - P
> Could not find angle parameter: CT - OS - O2
> Could not find angle parameter: H5 - CK - P
> Could not find angle parameter: CK - P - O2
> Could not find angle parameter: CK - P - O2
> Could not find angle parameter: CK - P - OS
> Could not find angle parameter: NB - CK - P
> Could not find angle parameter: N* - CK - P
Missing angle parameters
> Building proper torsion parameters.
> ** No torsion terms for OS-O2-P-O2
> ** No torsion terms for OS-O2-P-OS
> ** No torsion terms for CT-OS-O2-P
> ** No torsion terms for H5-CK-P-O2
> ** No torsion terms for H5-CK-P-O2
> ** No torsion terms for H5-CK-P-OS
> ** No torsion terms for NB-CK-P-O2
> ** No torsion terms for NB-CK-P-O2
> ** No torsion terms for NB-CK-P-OS
> ** No torsion terms for N*-CK-P-O2
> ** No torsion terms for N*-CK-P-O2
> ** No torsion terms for N*-CK-P-OS
Missing dihedral parameters
> Building improper torsion parameters.
> old PREP-specified impropers:
> <6OG 7>: C4 C8 N9 C1'
> <6OG 7>: C5 N9 C4 N3
> <6OG 7>: N2 N3 C2 N1
> <6OG 7>: C2 H57 N2 H59
> <6OG 7>: C5 N1 C6 O6
> <6OG 7>: C6 C4 C5 N7
> <6OG 7>: H55 N9 C8 N7
> total 630 improper torsions applied
> 7 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved.
The prmtop will not be saved without specifying those parameters
listed above. They are not recognized by leap. Your frcmod file is
large, so I didn't go through all of these parameters carefully, but
the ones I checked did not appear to be defined in your frcmod file.
If I had to guess where these missing parameters were coming from, I'd
probably guess bonds across residues (since if you just created an
frcmod from the prepin file for the O6G residue, it would not
necessarily have parameters for the connections between O6G and
neighbouring residues if your atom types differed from "typical"
nucleic acid atom types. Whether or not this is correct, though,
you'll have to supply these parameters before a prmtop can be created.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 02 2010 - 10:00:04 PST
