Dear Asmita,
- You do not need to convert a mol2 file into off file
- You need to add the FF atom types in the mol2 file:
1 P1 2.915901 -1.933666 -0.325078 P 1 PC 1.3950
^^^
this is the FF atom type column.
i.e. if I follow the link:
http://q4md-forcefieldtools.org/REDDB/projects/F-60/script1.ff
set DA3.1.P type P
set DA3.1.O1P type O2
set DA3.1.O2P type O2
# etc...
- You also need to define the head & the tail of this central fragment:
i.e. if I follow the link:
http://q4md-forcefieldtools.org/REDDB/projects/F-60/script1.ff
set DA head DA.1.P
set DA tail DA.1.O3'
set DA.1 connect0 DA.1.P
set DA.1 connect1 DA.1.O3'
set DA.1 restype nucleic
I hope all that will be soon automatically generated...
regards, Francois
> 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 Fri Jun 15 2012 - 12:00:03 PDT
