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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Received on Thu Jun 14 2012 - 11:30:03 PDT
