Dear Asmita,
The new base you are parametrizing is a tricky case: at the N3
position you have added a hydrogen atom: if I understand you (I did
not check again your data) the total charge of the new nucleobase is
consequently +1.
The atom types of cytosine were defined for the ... regular cytosine.
See the original paper (Cornell et al. JACS 1995, ...)
If you add a hydrogen atom at the N3 position (the atom type of this
hydrogen atom could be "H" by analogy to that found in the NALA
residue for instance) but it is likely you have to modify/adapt the
atom type at the N3 position itself (this is normal NC-H does not
exist as NC is used in regular nucleosides); moreover, as the
nucleobase is aromatic/conjugated I wonder what is the impact of this
hydrogen at N3 on the other atoms such as N1...
In your case, I would carefully study the atom types in the regular
nucleosides and from here make 'empirical' choices; what atom types at
N3, at N1 and what would be the FF dihedral parameter between the
deoxyribose and this new nucleobase.
regards, Francois
- CT - OS - HO ? This is meaningless: 'OS' is for ether/ester while HO
is for alcoholic hydrogen atoms: do you mean CT - OH - HO ?
Here you need to understand the meaning of the atom types (vs organic
functions) and stop using a black box to generate these FF atom types...
- the bonds are defined in the mol2 file generated by R.E.D. (from the
definition you made in the P2N file): if correctly defined you should
not need to add a new bond; if you need to add a new bond in LEaP this
means LEaP made some modifications reflecting a more important problem.
> 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?
>
> 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...
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 26 2012 - 01:00:04 PDT
