Some description in the previous off file was missing. Here is the complete
off file.
!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
"H35" "H1" 0 -1 0.0
"H36" "H1" 0 -1 0.0
entry.6OG.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.6OG.unit.childsequence single int
7
!entry.6OG.unit.connect array int
0
32
!entry.6OG.unit.connectivity table int atom1x int atom2x int flags
29 30 1
29 31 1
27 28 1
27 29 1
27 32 1
25 26 1
22 23 1
22 24 1
21 22 1
21 25 1
20 21 1
19 33 1
19 34 1
19 35 1
18 19 1
18 20 1
17 18 1
17 26 1
16 17 1
14 15 1
14 16 1
13 14 1
13 26 1
11 12 1
11 13 1
11 29 1
10 11 1
8 9 1
8 10 1
8 27 1
5 6 1
5 7 1
5 8 1
4 5 1
1 2 1
1 3 1
1 4 1
!entry.6OG.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 32
"R" 1 "A" 31
"R" 1 "A" 30
"R" 1 "A" 29
"R" 1 "A" 28
"R" 1 "A" 27
"R" 1 "A" 26
"R" 1 "A" 25
"R" 1 "A" 24
"R" 1 "A" 23
"R" 1 "A" 22
"R" 1 "A" 21
"R" 1 "A" 20
"R" 1 "A" 19
"R" 1 "A" 18
"R" 1 "A" 17
"R" 1 "A" 16
"R" 1 "A" 15
"R" 1 "A" 14
"R" 1 "A" 13
"R" 1 "A" 12
"R" 1 "A" 11
"R" 1 "A" 10
"R" 1 "A" 9
"R" 1 "A" 8
"R" 1 "A" 7
"R" 1 "A" 6
"R" 1 "A" 5
"R" 1 "A" 4
"R" 1 "A" 3
"R" 1 "A" 2
"R" 1 "A" 1
"R" 1 "A" 33
"R" 1 "A" 34
"R" 1 "A" 35 ""
!entry.6OG.unit.positions table dbl x dbl y dbl z
-12.881000 17.181000 28.328000
-13.011000 15.875000 27.620000
-14.010000 17.687000 29.147000
-11.565000 17.193000 29.224000
-10.278000 17.196000 28.593000
-10.235343 18.009065 27.868289
-10.138792 16.244641 28.079542
-9.175000 17.378000 29.609000
-8.203820 17.102210 29.198089
-9.037000 18.772000 29.959000
-9.486000 18.978000 31.289000
-8.629545 19.195248 31.927269
-10.255000 20.211000 31.314000
-11.619000 20.336000 31.321000
-12.257670 19.465493 31.294187
-12.017000 21.579000 31.360000
-10.839000 22.317000 31.380000
-10.637000 23.715000 31.434000
-11.488000 24.609000 31.475000
-9.284000 24.041000 31.440000
-8.254000 23.138000 31.395000
-7.011000 23.658000 31.401000
-6.761551 24.636455 31.423398
-6.246304 22.999522 31.359201
-8.429000 21.823000 31.346000
-9.742000 21.489000 31.345000
-9.481000 16.668000 30.920000
-10.107347 15.782651 30.810701
-10.230000 17.722000 31.708000
-11.267151 17.412068 31.835907
-9.764605 17.844232 32.686042
-8.268000 16.291000 31.572000
-10.857911 25.642776 32.069733
-11.937176 25.916000 32.204285
-10.194702 25.287186 31.943398
!entry.6OG.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
1 32 0 0 0 0
!entry.6OG.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"DG" 6 37 1 "n" 0
!entry.6OG.unit.residuesPdbSequenceNumber array int
1
!entry.6OG.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.6OG.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
On Fri, Mar 26, 2010 at 11:13 AM, 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
> !entry.6OG.unit.connectivity table int atom1x int atom2x int flags
> 29 30 1
> 29 31 1
> 27 28 1
> 27 29 1
> 27 32 1
> 25 26 1
> 22 23 1
> 22 24 1
> 21 22 1
> 21 25 1
> 20 21 1
> 19 33 1
> 19 34 1
> 19 35 1
> 18 19 1
> 18 20 1
> 17 18 1
> 17 26 1
> 16 17 1
> 14 15 1
> 14 16 1
> 13 14 1 5 6 1
> 5 7 1
> 5 8 1
> 4 5 1
> 1 2 1
> 1 3 1
> 1 4 1
> !entry.6OG.unit.hierarchy table str abovetype int abovex str belowtype
> int belowx
> "U" 0 "R" 1
> "R" 1 "A" 32
> "R" 1 "A" 31
> "R" 1 "A" 30
> "R" 1 "A" 29
> "R" 1 "A" 28
> "R" 1 "A" 27
> "R" 1 "A" 26
> "R" 1 "A" 25
> "R" 1 "A" 24
> "R" 1 "A" 23
> "R" 1 "A" 22
> "R" 1 "A" 21
> "R" 1 "A" 20
> "R" 1 "A" 19
> "R" 1 "A" 18
> "R" 1 "A" 17
> "R" 1 "A" 16
> "R" 1 "A" 15
> "R" 1 "A" 14
> "R" 1 "A" 13
> "R" 1 "A" 12
> "R" 1 "A" 11
> "R" 1 "A" 10 "R" 1 "A" 3
> "R" 1 "A" 2
> "R" 1 "A" 1
> "R" 1 "A" 33
> "R" 1 "A" 34
> "R" 1 "A" 35
> !entry.6OG.unit.name single str
> ""
> !entry.6OG.unit.positions table dbl x dbl y dbl z
> -12.881000 17.181000 28.328000
> -13.011000 15.875000 27.620000
> -14.010000 17.687000 29.147000
> -11.565000 17.193000 29.224000
> -10.278000 17.196000 28.593000
> -10.235343 18.009065 27.868289
> -10.138792 16.244641 28.079542
> -9.175000 17.378000 29.609000
> -8.203820 17.102210 29.198089
> -9.037000 18.772000 29.959000
> -9.486000 18.978000 31.289000
> -8.629545 19.195248 31.927269
> -10.255000 20.211000 31.314000
> -11.619000 20.336000 31.321000
> -12.257670 19.465493 31.294187
> -12.017000 21.579000 31.360000
> -10.839000 22.317000 31.380000
> -10.637000 23.715000 31.434000
> -11.488000 24.609000 31.475000
> -9.284000 24.041000 31.440000
> -8.254000 23.138000 31.395000
> -7.011000 23.658000 31.401000
> -6.761551 24.636455 31.423398
> -6.246304 22.999522 31.359201
> -8.429000 21.823000 31.346000
> -9.742000 21.489000 31.345000
> -9.481000 16.668000 30.920000
> -10.107347 15.782651 30.810701
> -10.230000 17.722000 31.708000
> -11.267151 17.412068 31.835907
> -9.764605 17.844232 32.686042
> -8.268000 16.291000 31.572000
> -10.857911 25.642776 32.069733
> -11.937176 25.916000 32.204285
> -10.194702 25.287186 31.943398
> !entry.6OG.unit.residueconnect table int c1x int c2x int c3x int c4x
> int c5x int c6x
> 1 32 0 0 0 0
> !entry.6OG.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> "DG" 6 37 1 "n" 0
> !entry.6OG.unit.residuesPdbSequenceNumber array int
> 1
> !entry.6OG.unit.solventcap array dbl
> -1.000000
> 0.0
> 0.0
> 0.0
> 0.0
> !entry.6OG.unit.velocities table dbl x dbl y dbl z
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 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>
> 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
>>
>
>
>
> -
>
--
Nihar Ranjan Jena
Research Scientist,
SERC Fast Track Scheme for Young Scientists (DST)
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012, India
Web page: http://sites.google.com/site/nrjena/Home
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 25 2010 - 23:00:07 PDT
