AMBER Archive (2006)

Subject: AMBER: atom type "O3" not recognized by XLeap

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Fri Jan 27 2006 - 11:32:48 CST

Dear AMBER community:

I am trying to use the ADP parameters downloaded from the AMBER website; the
parameters of Meagher KL, Redman LT, Carlson HA* Journal of Computational
Chemistry* *2003*,*24*,1016. For some reason when I try to build the prmtop
and inpcrd files, XLeap claims that it does not recognize the atoms "O1B",
"O2B", and "O3B" of the atom type "O3". I have used the ATP parameters
downloaded from the website which also use the atom type "O3", and with the
ATP I didn't have any trouble. Does anyone have any idea what might be
causing the problem? I have cut and pasted the prep file (which I downloaded
from the website) and the library file (which I am using in XLeap) below. I
have attached the pdb file that I am using. I would be very grateful for any
suggestions.

Thank you in advance for your help.

Kenley

PREP FILE

    0 0 2

R-ADENOSINE - with diphosphate linker
adp.db94
 adp INT 1
 CORRECT OMIT DU BEG
   0.0
    1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000
    2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000
    3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.000
    4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552
    5 PB P M 4 3 2 1.434 90.000 180.000 1.3672
    6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552
    7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552
    8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346
    9 PA P M 6 5 4 1.646 130.619 36.624 1.4929
   10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474
   11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474
   12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579
   13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558
   14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679
   15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679
   16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065
   17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174
   18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548
   19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394
   20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007
   21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251
   22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006
   23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553
   24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073
   25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515
   26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009
   27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019
   28 H60 H E 27 26 25 1.010 120.010 2.829 0.4115
   29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115
   30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615
   31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875
   32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473
   33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997
   34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053
   35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022
   36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615
   37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541
   38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376
   39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670
   40 H20 H1 E 39 35 16 1.059 115.086 78.119 0.0972
   41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139
   42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186

IMPROPER
 C8 C4 N9 C1*
 C6 H60 N6 H61
 N7 N9 C8 H80
 N1 N3 C2 H2
 C5 N1 C6 N6

LOOP CLOSING EXPLICIT
 C1* C2*
 C4 C5
 C4 N9

DONE
STOP

LIBRARY FILE

!!index array str
 "adp"
!entry.adp.unit.atoms table str name str type int typex int resx int
flags
 int seq int elmnt dbl chg
 "O1B" "O3" 0 1 131072 1 -1 -0.955200
 "PB" "P" 0 1 131072 2 15 1.367200
 "O2B" "O3" 0 1 131072 3 -1 -0.955200
 "O3B" "O3" 0 1 131072 4 -1 -0.955200
 "O3A" "OS" 0 1 131072 5 8 -0.634600
 "PA" "P" 0 1 131072 6 15 1.492900
 "O1A" "O2" 0 1 131072 7 8 -0.947400
 "O2A" "O2" 0 1 131072 8 8 -0.947400
 "O5*" "OS" 0 1 131072 9 8 -0.657900
 "C5*" "CT" 0 1 131072 10 6 0.055800
 "H50" "H1" 0 1 131072 11 1 0.067900
 "H51" "H1" 0 1 131072 12 1 0.067900
 "C4*" "CT" 0 1 131072 13 6 0.106500
 "H40" "H1" 0 1 131072 14 1 0.117400
 "O4*" "OS" 0 1 131072 15 8 -0.354800
 "C1*" "CT" 0 1 131072 16 6 0.039400
 "H10" "H2" 0 1 131072 17 1 0.200700
 "N9" "N*" 0 1 131072 18 7 -0.025100
 "C8" "CK" 0 1 131072 19 6 0.200600
 "H80" "H5" 0 1 131072 20 1 0.155300
 "N7" "NB" 0 1 131072 21 7 -0.607300
 "C5" "CB" 0 1 131072 22 6 0.051500
 "C6" "CA" 0 1 131072 23 6 0.700900
 "N6" "N2" 0 1 131072 24 7 -0.901900
 "H60" "H" 0 1 131072 25 1 0.411500
 "H61" "H" 0 1 131072 26 1 0.411500
 "N1" "NC" 0 1 131072 27 7 -0.761500
 "C2" "CQ" 0 1 131072 28 6 0.587500
 "H2" "H5" 0 1 131072 29 1 0.047300
 "N3" "NC" 0 1 131072 30 7 -0.699700
 "C4" "CB" 0 1 131072 31 6 0.305300
 "C3*" "CT" 0 1 131072 32 6 0.202200
 "H30" "H1" 0 1 131072 33 1 0.061500
 "O3*" "OH" 0 1 131072 34 8 -0.654100
 "H3*" "HO" 0 1 131072 35 1 0.437600
 "C2*" "CT" 0 1 131072 36 6 0.067000
 "H20" "H1" 0 1 131072 37 1 0.097200
 "O2*" "OH" 0 1 131072 38 8 -0.613900
 "H2*" "HO" 0 1 131072 39 1 0.418600
!entry.adp.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "O1B" "O3" 0 -1 0.0
 "PB" "P" 0 -1 0.0
 "O2B" "O3" 0 -1 0.0
 "O3B" "O3" 0 -1 0.0
 "O3A" "OS" 0 -1 0.0
 "PA" "P" 0 -1 0.0
 "O1A" "O2" 0 -1 0.0
 "O2A" "O2" 0 -1 0.0
 "O5*" "OS" 0 -1 0.0
 "C5*" "CT" 0 -1 0.0
 "H50" "H1" 0 -1 0.0
 "H51" "H1" 0 -1 0.0
 "C4*" "CT" 0 -1 0.0
 "H40" "H1" 0 -1 0.0
 "O4*" "OS" 0 -1 0.0
 "C1*" "CT" 0 -1 0.0
 "H10" "H2" 0 -1 0.0
 "N9" "N*" 0 -1 0.0
 "C8" "CK" 0 -1 0.0
 "H80" "H5" 0 -1 0.0
 "N7" "NB" 0 -1 0.0
 "C5" "CB" 0 -1 0.0
 "C6" "CA" 0 -1 0.0
 "N6" "N2" 0 -1 0.0
 "H60" "H" 0 -1 0.0
 "H61" "H" 0 -1 0.0
 "N1" "NC" 0 -1 0.0
 "C2" "CQ" 0 -1 0.0
 "H2" "H5" 0 -1 0.0
 "N3" "NC" 0 -1 0.0
 "C4" "CB" 0 -1 0.0
 "C3*" "CT" 0 -1 0.0
 "H30" "H1" 0 -1 0.0
 "O3*" "OH" 0 -1 0.0
 "H3*" "HO" 0 -1 0.0
 "C2*" "CT" 0 -1 0.0
 "H20" "H1" 0 -1 0.0
 "O2*" "OH" 0 -1 0.0
 "H2*" "HO" 0 -1 0.0
!entry.adp.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.adp.unit.childsequence single int
 2
!entry.adp.unit.connect array int
 1
 36
!entry.adp.unit.connectivity table int atom1x int atom2x int flags
 1 2 1
 2 3 1
 2 4 1
 2 5 1
 5 6 1
 6 7 1
 6 8 1
 6 9 1
 9 10 1
 10 11 1
 10 12 1
 10 13 1
 13 14 1
 13 15 1
 13 32 1
 15 16 1
 16 17 1
 16 18 1
 16 36 1
 18 19 1
 18 31 1
 19 20 1
 19 21 1
 21 22 1
 22 23 1
 22 31 1
 23 24 1
 23 27 1
 24 25 1
 24 26 1
 27 28 1
 28 29 1
 28 30 1
 30 31 1
 32 33 1
 32 34 1
 32 36 1
 34 35 1
 36 37 1
 36 38 1
 38 39 1
!entry.adp.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
 "R" 1 "A" 4
 "R" 1 "A" 5
 "R" 1 "A" 6
 "R" 1 "A" 7
 "R" 1 "A" 8
 "R" 1 "A" 9
 "R" 1 "A" 10
 "R" 1 "A" 11
 "R" 1 "A" 12
 "R" 1 "A" 13
 "R" 1 "A" 14
 "R" 1 "A" 15
 "R" 1 "A" 16
 "R" 1 "A" 17
 "R" 1 "A" 18
 "R" 1 "A" 19
 "R" 1 "A" 20
 "R" 1 "A" 21
 "R" 1 "A" 22
 "R" 1 "A" 23
 "R" 1 "A" 24
 "R" 1 "A" 25
 "R" 1 "A" 26
 "R" 1 "A" 27
 "R" 1 "A" 28
 "R" 1 "A" 29
 "R" 1 "A" 30
 "R" 1 "A" 31
 "R" 1 "A" 32
 "R" 1 "A" 33
 "R" 1 "A" 34
 "R" 1 "A" 35
 "R" 1 "A" 36
 "R" 1 "A" 37
 "R" 1 "A" 38
 "R" 1 "A" 39
!entry.adp.unit.name single str
 "adp"
!entry.adp.unit.positions table dbl x dbl y dbl z
 2.000001 1.000000 -1.346410E-06
 2.000002 2.434000 5.843420E-07
 1.724903 2.907052 -1.475810
 3.300363 3.146821 0.324455
 3.467779 3.068374 -2.513991E-06
 4.849242 2.573067 -0.745353
 5.603590 1.650945 0.172616
 4.495749 2.078354 -2.144988
 5.586580 3.976117 -0.748172
 5.106841 5.098759 -1.521185
 4.058873 5.016981 -1.649856
 5.579658 5.101927 -2.468770
 5.376379 6.403922 -0.884454
 4.967680 7.131864 -1.536027
 4.623643 6.405463 0.392147
 5.507939 6.765371 1.403763
 5.483837 7.815750 1.536442
 5.089507 5.910142 2.629407
 4.575858 4.624186 2.534398
 4.331661 4.021157 1.674859
 4.381054 4.122269 3.809383
 4.787407 5.176469 4.627652
 4.776061 5.243868 6.037996
 4.297026 4.311429 6.861387
 3.935667 3.445296 6.488113
 4.295233 4.470651 7.857743
 5.260117 6.400634 6.518862
 5.739486 7.380635 5.740786
 6.146204 8.272596 6.186783
 5.767139 7.364260 4.364161
 5.251880 6.241203 3.960117
 6.792265 6.725736 -0.577931
 7.544648 6.249588 -1.151241
 6.959409 8.120797 -0.652202
 7.781479 8.370989 -0.208701
 6.914541 6.308625 0.969168
 7.011269 5.269270 1.147682
 7.893677 6.998460 1.690155
 8.691108 7.083998 1.149900
!entry.adp.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 1 36 0 0 0 0
!entry.adp.unit.residues table str name int seq int childseq int
startatomx
 str restype int imagingx
 "adp" 1 40 1 "?" 0
!entry.adp.unit.residuesPdbSequenceNumber array int
 0
!entry.adp.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.adp.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
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0


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