Dear Francois,
I manually edited the mol2 file to add the amber12
(ff12SB) atom types. Now, since ff12SB loads nucleic10.lib which does not
contain atom type for H3 atom (protonation at N3), what type should i give
here. When i kept the atom type as 'H' and loaded the resulting mol2 file
in tleap, i got a missing parameter error :
Checking parameters for unit 'PC'.
Checking for bond parameters.
Could not find bond parameter for: NC - H
Checking for angle parameters.
Could not find angle parameter: CT - OS - HO
Could not find angle parameter: C - NC - H
Could not find angle parameter: H - NC - CA
There are missing parameters.
Unit is OK.
It seems that everything else is fine except bond and angles involving H3.
I also tried to add the missing bond using "bond" command in tleap but it
also resulted in an error :
bond c.24.N24 c.25.H25
bond: Argument #1 is type String must be of type: [atom]
Is the syntax of the bond command right?
Asmita
On Sat, Jun 16, 2012 at 12:22 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Mon Jun 25 2012 - 10:30:03 PDT
