You seem to have lost atom types (perhaps) from the original definition.
My suggestion is to compare your mol2/OFF file to the nucleic10.lib to
make sure that the atom names and types line up as much as possible
(obviously around the protonation site N3 they may not match up, but
elsewhere they should).
Then, use parmchk (described in the AmberTools manual) to find any missing
parameters, which you will then have to fill in.
HTH,
Jason
On Thu, Jun 14, 2012 at 2:24 PM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear Users,
>
> I want to generate force field library files for an N3-protonated cytosine.
> For that, i used RED server (AnteRed for P2N file), gaussian 09 for
> goemetry optimization and finally RED tools for mol2 file generation. I
> created a .lib file on the lines of script given here :
> http://q4md-forcefieldtools.org/REDDB/projects/F-60/script1.ff. But after
> loading the resulting .lib file, tleap still is unable to recognize the
> modified residue in the PDB file and i get an error like this :
>
> Creating new UNIT for residue: PC sequence: 6
> Created a new atom named: P within residue: .R<PC 6>
> Created a new atom named: O1P within residue: .R<PC 6>
> Created a new atom named: O2P within residue: .R<PC 6>
> Created a new atom named: O5' within residue: .R<PC 6>
> Created a new atom named: C5' within residue: .R<PC 6>
> Created a new atom named: C4' within residue: .R<PC 6>
> .
> .
> .
> The problem was still there when i tried to load mol2 file directly as a
> force field library. I checked my mol2 file using check command in tleap
> and an error message is coming like :
>
> Could not find bond parameter for: O - H
> Could not find bond parameter for: O - H
> Could not find bond parameter for: C - H
> Could not find bond parameter for: C - H
> Checking for angle parameters.
> Could not find angle parameter: P - O - C
> Could not find angle parameter: O - P - O
> Could not find angle parameter: O - P - O
> Could not find angle parameter: O - P - O
> Could not find angle parameter: O - C - H
> Could not find angle parameter: O - C - H
> Could not find angle parameter: C - C - H
> Could not find angle parameter: C - C - C
> Could not find angle parameter: H - C - H
> Could not find angle parameter: H - C - C
> Could not find angle parameter: H - C - C
> Could not find angle parameter: C - O - C
> Could not find angle parameter: C - C - C
> Could not find angle parameter: C - C - H
> Could not find angle parameter: H - C - O
> Could not find angle parameter: H - C - C
> Could not find angle parameter: O - C - H
> Could not find angle parameter: C - C - H
> Could not find angle parameter: C - C - C
> Could not find angle parameter: C - N - C
> Could not find angle parameter: C - N - C
> Could not find angle parameter: H - C - C
> Could not find angle parameter: H - C - N
> Could not find angle parameter: C - C - N
> Could not find angle parameter: C - C - H
> Could not find angle parameter: C - O - H
> Could not find angle parameter: H - C - C
> Could not find angle parameter: H - C - O
> Could not find angle parameter: C - O - H
> Could not find angle parameter: H - C - O
> Could not find angle parameter: N - C - N
> Could not find angle parameter: N - C - C
> Could not find angle parameter: N - C - H
> Could not find angle parameter: C - N - C
> Could not find angle parameter: C - N - C
> Could not find angle parameter: N - C - N
> Could not find angle parameter: N - C - C
> Could not find angle parameter: C - C - H
> Could not find angle parameter: C - C - C
> Could not find angle parameter: N - C - C
> Could not find angle parameter: C - C - H
> Could not find angle parameter: H - C - C
> There are missing parameters.
> Unit is OK.
>
> What am i missing over here? I am attaching some files for reference...
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 14 2012 - 12:30:02 PDT
