Hello,
see my comments below:
On Thu, Mar 25, 2010 at 10:43 PM, N.R. Jena <nrjena.gmail.com> wrote:
> Dear Prof. David,
> As you suggested we created N-methyl guanine molecule and hence .frcmod file
> for it. Then we created an .off file for the complete nucleotide as follows.
> However, while loading in tleap, it is complaining about the unknown
> residues. That means it is unable to read the off file. What may be the
> cause? Here the residue 7 is connected to 6 and 8 residues (tail and head)
> respectively.
>
>
> !entry.6OG.unit.atoms table str name str type int typex int resx int
> flags int seq int elmnt dbl chg
> "P" "P" 0 1 131073 1 15 1.165900
> "O1P" "O2" 0 1 131073 2 8 -0.776100
> "O2P" "O2" 0 1 131073 3 8 -0.776100
> "O5'" "OS" 0 1 131073 4 8 -0.495400
> "C5'" "CT" 0 1 131073 5 6 -0.006900
> "H5'1" "H1" 0 1 131073 6 1 0.075400
> "H5'2" "H1" 0 1 131073 7 1 0.075400
> "C4'" "CT" 0 1 131073 8 6 0.162900
> "H4'" "H1" 0 1 131073 9 1 0.117600
> "O4'" "OS" 0 1 131073 10 8 -0.369100
> "C1'" "CT" 0 1 131073 11 6 0.035800
> "H1'" "H2" 0 1 131073 12 1 0.174600
> "N9" "N*" 0 1 131073 13 7 -0.270650
> "C8" "CK" 0 1 131073 14 6 0.389590
> "H8" "H5" 0 1 131073 15 1 0.072010
> "N7" "NB" 0 1 131073 16 7 -0.500790
> "C5" "CB" 0 1 131073 17 6 -0.217060
> "C6" "CT" 0 1 131073 18 6 0.753910
> "O6" "OS" 0 1 131073 19 8 -0.416830
> "N1" "NC" 0 1 131073 20 7 -0.837170
> "C2" "CQ" 0 1 131073 22 6 0.913420
> "N2" "N2" 0 1 131073 23 7 -0.827130
> "H21" "H" 0 1 131073 24 1 0.427860
> "H22" "H" 0 1 131073 25 1 0.427730
> "N3" "NC" 0 1 131073 26 7 -0.646660
> "C4" "CB" 0 1 131073 27 6 0.476730
> "C3'" "CT" 0 1 131073 28 6 0.071300
> "H3'" "H1" 0 1 131073 29 1 0.098500
> "C2'" "CT" 0 1 131073 30 6 -0.085400
> "H2'1" "HC" 0 1 131073 31 1 0.071800
> "H2'2" "HC" 0 1 131073 32 1 0.071800
> "O3'" "OS" 0 1 131073 33 8 -0.523200
> "H34" "H1" 0 1 17825793 34 1 0.065670
> "H35" "H1" 0 1 17825793 35 1 0.045470
> "H36" "H1" 0 1 17825793 36 1 0.047840
> !entry.6OG.unit.atomspertinfo table str pname str ptype int ptypex int
> pelmnt dbl pchg
> "P" "P" 0 -1 0.0
> "O1P" "O2" 0 -1 0.0
> "O2P" "O2" 0 -1 0.0
> "O5'" "OS" 0 -1 0.0
> "C5'" "CT" 0 -1 0.0
> "H5'1" "H1" 0 -1 0.0
> "H5'2" "H1" 0 -1 0.0
> "C4'" "CT" 0 -1 0.0
> "H4'" "H1" 0 -1 0.0
> "O4'" "OS" 0 -1 0.0
> "C1'" "CT" 0 -1 0.0
> "H1'" "H2" 0 -1 0.0
> "N9" "N*" 0 -1 0.0
> "C8" "CK" 0 -1 0.0
> "H8" "H5" 0 -1 0.0
> "N7" "NB" 0 -1 0.0
> "C5" "CB" 0 -1 0.0
> "C6" "CT" 0 -1 0.0
> "O6" "OS" 0 -1 0.0
> "N1" "NC" 0 -1 0.0
> "C2" "CQ" 0 -1 0.0
> "N2" "N2" 0 -1 0.0
> "H21" "H" 0 -1 0.0
> "H22" "H" 0 -1 0.0
> "N3" "NC" 0 -1 0.0
> "C4" "CB" 0 -1 0.0
> "C3'" "CT" 0 -1 0.0
> "H3'" "H1" 0 -1 0.0
> "C2'" "CT" 0 -1 0.0
> "H2'1" "HC" 0 -1 0.0
> "H2'2" "HC" 0 -1 0.0
> "O3'" "OS" 0 -1 0.0
> "H34" "H1" 0 -1 0.0 0.0
> 0.0
> !entry.6OG.unit.childsequence single int
> 7
> !entry.6OG.unit.connect array int
> 0
> 32
This connectivity suggests that there is only one atom connected to
atom name O3. Thus, this would be a 5' nucleic acid terminal residue
according to the existing nucleic acid OFF library files. Also, your
template has 35 atoms. Atoms 33-35 (after the O3) are all hydrogens.
Make sure that atom 32 doesn't have any hydrogens bonded to it (since
it must be bonded to the 3' carbon and must not be bonded to anything
else so it can be bonded to the next residue).
> !entry.6OG.unit.connectivity table int atom1x int atom2x int flags
>
> cut
>
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> -------------------------------------------------------------------------------------------------------
> Creating new UNIT for residue: 6OG sequence: 7
> One sided connection. Residue: missing connect0 atom.
> Created a new atom named: P within residue: .R<6OG 7>
> Created a new atom named: O1P within residue: .R<6OG 7>
> Created a new atom named: O2P within residue: .R<6OG 7>
> Created a new atom named: O5' within residue: .R<6OG 7>
> Created a new atom named: N9 within residue: .R<6OG 7>
> Created a new atom named: C4 within residue: .R<6OG 7>
> Created a new atom named: N3 within residue: .R<6OG 7>
> Created a new atom named: C2 within residue: .R<6OG 7>
> Created a new atom named: N2 within residue: .R<6OG 7>
> Created a new atom named: N1 within residue: .R<6OG 7>
> Created a new atom named: C6 within residue: .R<6OG 7>
> Created a new atom named: O6 within residue: .R<6OG 7>
> Created a new atom named: C within residue: .R<6OG 7>
> Created a new atom named: C5 within residue: .R<6OG 7>
> Created a new atom named: N7 within residue: .R<6OG 7>
> Created a new atom named: C8 within residue: .R<6OG 7>
> Created a new atom named: C2' within residue: .R<6OG 7>
> Created a new atom named: C5' within residue: .R<6OG 7>
> Created a new atom named: C4' within residue: .R<6OG 7>
> Created a new atom named: O4' within residue: .R<6OG 7>
> Created a new atom named: C1' within residue: .R<6OG 7>
> Created a new atom named: C3' within residue: .R<6OG 7>
> Created a new atom named: O3' within residue: .R<6OG 7>
This suggests that the atom names in your PDB file does not match the
names in your library file. Also, considering the fact that the 6OG
is your 7th residue, I'm guessing you did not mean for it to be a 5'
terminus. I would be willing to bet that your library file is
incorrect. You may visualize it easily by loading that library file
in xleap and using the command "edit 6OG". This should bring up an
x-window with that residue displayed. You should check to make sure
it is what you want it to be.
Good luck!
Jason
> One sided connection. Residue: missing connect1 atom.
> Added missing heavy atom: .R<DT 14>.A<P 1>
> Added missing heavy atom: .R<DT 14>.A<O1P 2>
> Added missing heavy atom: .R<DT 14>.A<O2P 3>
> total atoms in file: 1697
> Leap added 1472 missing atoms according to residue templates:
>
> On Mon, Feb 1, 2010 at 9:34 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Mon, Feb 01, 2010, Jason Swails wrote:
>> >
>> > There is an option in antechamber to specify Amber atom types, though
>> > having never used it on nucleotides before, I don't know exactly how
>> > well it works (i.e. whether it will be compatible with the way Amber
>> > names nucleic acid atom types).
>>
>> When one is making a modification to an existing residue (such as in your
>> case), it is generally recommended (by me!) to ask antechamber to use Amber
>> atom types, not gaff ones. In this way, all the unchanged parts (including
>> the connections between your new residue and its surroundings) will be the
>> same as in the standard nucleotides, and you just have to check the
>> parameters
>> involving the O-methyl part.
>>
>> It is also trickier to generate Amber files for a fragment (like a
>> nucleotide
>> that is to be inserted in a DNA chain) than for a complete molecule (which
>> has
>> no dangling bonds). Here's what I would do:
>>
>> 1. Make a "complete molecule" to use with antechamber. I would suggest
>> N9-methyl guanine with the O6 modification. Run this through antechamber
>> (use amber atom types) to get charges and force field parameters. (Or, use
>> R.E.D. to get charges.)
>>
>> 2. Using xleap, copy the existing guanine nucleotide to a unit with
>> whatever
>> new name you want, then edit this new unit, manually creating the
>> needed modifications for O-methylation. Select all atoms, and go to "edit
>> selected atoms", where you can manually enter the charges you got from step
>> 1. You may want to make small modifications to keep most of the atoms with
>> the same charges, and you will need to also make adjustments to make sure
>> the
>> total charge is correct. Save the results as an off file.
>>
>> 3. Now you can load this off file along with the usual force fields, and
>> load
>> whatever frcmod file you got from step 1.
>>
>> ...hope this helps....dac
>>
>>
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>>
>
>
>
> -
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Mar 26 2010 - 00:00:02 PDT
