It is fixed now. Thank u all for the guidance.
On Fri, Mar 26, 2010 at 12:02 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > -
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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 - 06:00:20 PDT
