AMBER Archive (2006)

Subject: AMBER: xleap not recognizing residue

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Sun May 07 2006 - 19:13:13 CDT

Dear AMBER community,

I just created a new library file for a methylated histidine. Initially
everything appeared to be fine (XLeap read in the pdb file containing the
methylated histidine without complaining), but then when I tried to set the
connect0 and connect1 atoms XLeap told me that "HMH", my residue name, was
not a residue:

> no = loadpdb "1j6z_salt_test.pdb"
Loading PDB file: ./1j6z_salt_test.pdb
 (starting new molecule for chain B)
  Added missing heavy atom: .R<NGLU 4>.A<CG 10>
  Added missing heavy atom: .R<NGLU 4>.A<CD 13>
  Added missing heavy atom: .R<NGLU 4>.A<OE1 14>
  Added missing heavy atom: .R<NGLU 4>.A<OE2 15>
  Added missing heavy atom: .R<CARG 372>.A<OXT 25>
  total atoms in file: 3315
  Leap added 3680 missing atoms according to residue templates:
       5 Heavy
       3675 H / lone pairs
> set no.HMH connect0 no.HMH.N
no.HMH: not a container (e.g. residue)
usage: set <container> <parameter> <object>
   or: set default <parameter> <value>

After being unable to set the connect0 and connect1 atoms, I tried to save
the inpcrd and prmtop files, and XLeap gave this complaint:

 (Residues lacking connect0/connect1 -
   these don't have chain types marked:

    res total affected

                 1
    CARG 1
    NGLU 1
    WAT 404
  )

Presumably the " 1" refers to my methylated histidine. I'm not sure why
XLeap isn't recognizing the residue name. I have cut and pasted the library
file below, and I would be very grateful if anyone would look and give me
suggestions. I have attached the pdb file.

Thank you in advance for any advice.

Kenley

!!index array str
 "HMH"
 "e"
!entry.HMH.unit.atoms table str name str type int typex int resx int
flags
 int seq int elmnt dbl chg
 "C1" "CT" 0 1 131072 1 6 -0.193000
 "H11" "H1" 0 1 131072 2 1 0.100000
 "H12" "H1" 0 1 131072 3 1 0.100000
 "H13" "H1" 0 1 131072 4 1 0.100000
 "NE2" "N*" 0 1 131072 5 7 0.167000
 "CD2" "CA" 0 1 131072 6 6 -0.347000
 "HD2" "H4" 0 1 131072 7 1 0.196000
 "CE1" "CK" 0 1 131072 8 6 0.030000
 "HE1" "H5" 0 1 131072 9 1 0.132000
 "ND1" "NB" 0 1 131072 10 7 -0.483000
 "CG" "CC" 0 1 131072 11 6 0.261000
 "CB" "CT" 0 1 131072 12 6 -0.196000
 "HB3" "HC" 0 1 131072 13 1 0.089000
 "HB2" "HC" 0 1 131072 14 1 0.089000
 "CA" "CT" 0 1 131072 15 6 -0.057000
 "C" "C" 0 1 131072 16 6 0.541000
 "O" "O" 0 1 131072 17 8 -0.581000
 "HA" "H1" 0 1 131072 21 1 0.129000
 "N" "N" 0 1 131072 22 7 -0.231000
 "H" "H" 0 1 131072 23 1 0.154000
!entry.HMH.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "C15" "CT" 0 -1 0.0
 "H16" "H1" 0 -1 0.0
 "H17" "H1" 0 -1 0.0
 "H18" "H1" 0 -1 0.0
 "N14" "N*" 0 -1 0.0
 "C19" "CA" 0 -1 0.0
 "H20" "H4" 0 -1 0.0
 "C12" "CK" 0 -1 0.0
 "H13" "H5" 0 -1 0.0
 "N11" "NB" 0 -1 0.0
 "C10" "CC" 0 -1 0.0
 "C07" "CT" 0 -1 0.0
 "H08" "HC" 0 -1 0.0
 "H09" "HC" 0 -1 0.0
 "C03" "CT" 0 -1 0.0
 "C04" "C" 0 -1 0.0
 "O05" "O" 0 -1 0.0
 "H06" "H1" 0 -1 0.0
 "N01" "N" 0 -1 0.0
 "H02" "H" 0 -1 0.0
!entry.HMH.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HMH.unit.childsequence single int
 2
!entry.HMH.unit.connect array int
 19
 16
!entry.HMH.unit.connectivity table int atom1x int atom2x int flags
 1 2 1
 1 3 1
 1 4 1
 1 5 1
 5 6 1
 5 8 1
 6 7 1
 6 11 1
 8 9 1
 8 10 1
 10 11 1
 11 12 1
 12 13 1
 12 14 1
 12 15 1
 15 16 1
 15 18 1
 15 19 1
 16 17 1
 19 20 1
!entry.HMH.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
!entry.HMH.unit.name single str
 "HMH"
!entry.HMH.unit.positions table dbl x dbl y dbl z
 3.536914 1.422858 -1.933042E-06
 4.136485 2.107826 0.584854
 2.563953 1.328008 0.459074
 3.417172 1.818598 -0.999889
 4.162503 0.116744 -0.048008
 5.393245 -0.182994 -0.575092
 6.017100 0.562471 -1.022292
 3.663564 -1.033407 0.425082
 2.702919 -1.083201 0.895955
 4.468370 -2.034816 0.247104
 5.568684 -1.511619 -0.388072
 6.736553 -2.370608 -0.769153
 7.580487 -1.744930 -1.032196
 7.030757 -2.972195 0.087063
 6.464347 -3.304974 -1.963952
 7.755660 -4.052496 -2.283949
 8.617789 -3.503782 -2.928084
 6.250199 -2.708327 -2.842042
 5.345104 -4.181003 -1.676957
 4.800657 -3.975992 -0.864831
!entry.HMH.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 1 0 0 0 0 0
!entry.HMH.unit.residues table str name int seq int childseq int
startatomx
 str restype int imagingx
 "" 1 27 1 "?" 0
!entry.HMH.unit.residuesPdbSequenceNumber array int
 0
!entry.HMH.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HMH.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
!entry.e.parm.angles table str type1 str type2 str type3 dbl kt dbl t0
str desc
 "CA" "N*" "CT" 62.700000 2.150421 ""
 "CK" "N*" "CT" 62.700000 2.150421 ""
 "H1" "CT" "H1" 35.000000 1.911136 ""
 "H1" "CT" "N*" 50.000000 1.911136 ""
 "H4" "CA" "N*" 50.000000 2.147629 ""
 "CC" "CA" "N*" 68.700000 1.940807 ""
 "H5" "CK" "N*" 50.000000 2.147629 ""
 "N*" "CK" "NB" 70.000000 2.087415 ""
 "CA" "N*" "CK" 67.700000 1.929462 ""
 "CA" "CC" "NB" 65.400000 2.086891 ""
 "CA" "CC" "CT" 61.400000 2.139600 ""
 "CC" "CA" "H4" 50.000000 2.094396 ""
 "CC" "NB" "CK" 70.000000 1.958260 ""
 "H5" "CK" "NB" 50.000000 2.147629 ""
 "CT" "CC" "NB" 64.463000 2.066471 ""
 "CC" "CT" "HC" 50.000000 1.911136 ""
 "CC" "CT" "CT" 63.000000 1.989676 ""
 "C" "CT" "CT" 63.000000 1.939062 ""
 "CT" "CT" "H1" 46.500000 1.919688 ""
 "CT" "CT" "N" 80.000000 1.914627 ""
 "HC" "CT" "HC" 35.000000 1.911136 ""
 "CT" "CT" "HC" 46.500000 1.919688 ""
 "CT" "C" "O" 80.000000 2.183757 ""
 "CT" "C" "N" 70.000000 2.035055 ""
 "CT" "N" "H" 45.800000 2.062980 ""
 "C" "N" "CT" 50.000000 2.127557 ""
 "C" "CT" "H1" 50.000000 1.911136 ""
 "C" "CT" "N" 63.000000 1.921608 ""
 "C" "N" "H" 47.600000 2.054952 ""
 "N" "C" "O" 80.000000 2.145011 ""
 "H" "N" "H" 35.000000 2.094396 ""
 "H1" "CT" "N" 50.000000 1.911136 ""
 "HA" "C" "N" 50.000000 2.094396 ""
 "HA" "C" "O" 50.000000 2.094396 ""
!entry.e.parm.atoms table str type dbl mass dbl e dbl r int element
int hybrid str desc dbl polar
 "CT" 12.010000 0.109400 1.908000 6 3 "" 0.878000
 "H1" 1.008000 0.015700 1.487000 1 3 "" 0.135000
 "N*" 14.010000 0.170000 1.824000 7 2 "" 0.530000
 "CA" 12.010000 0.086000 1.908000 6 2 "" 0.360000
 "H4" 1.008000 0.015700 1.487000 1 3 "" 0.135000
 "CK" 12.010000 0.086000 1.908000 6 2 "" 0.360000
 "H5" 1.008000 0.015700 1.487000 1 3 "" 0.135000
 "NB" 14.010000 0.170000 1.824000 7 2 "" 0.530000
 "CC" 12.010000 0.086000 1.908000 6 2 "" 0.360000
 "HC" 1.008000 0.015700 1.487000 1 3 "" 0.135000
 "C" 12.010000 0.086000 1.908000 6 2 "" 0.616000
 "O" 16.000000 0.210000 1.661200 8 2 "" 0.434000
 "N" 14.010000 0.170000 1.824000 7 2 "" 0.530000
 "H" 1.008000 0.015700 0.600000 1 3 "" 0.161000
 "HA" 1.008000 0.015700 1.487000 1 3 "" 0.135000
!entry.e.parm.bonds table str type1 str type2 dbl kb dbl r0 str desc
 "CT" "H1" 341.900000 1.089000 ""
 "CT" "N*" 343.100000 1.450000 ""
 "CA" "N*" 440.200000 1.370000 ""
 "CK" "N*" 440.200000 1.370000 ""
 "CA" "H4" 367.000000 1.080000 ""
 "CA" "CC" 473.700000 1.390000 ""
 "CK" "H5" 367.000000 1.080000 ""
 "CK" "NB" 399.300000 1.400000 ""
 "CC" "NB" 399.300000 1.400000 ""
 "CC" "CT" 330.300000 1.510000 ""
 "CT" "HC" 341.900000 1.089000 ""
 "CT" "CT" 307.600000 1.530000 ""
 "C" "CT" 326.400000 1.510000 ""
 "CT" "N" 330.600000 1.460000 ""
 "C" "O" 540.400000 1.260000 ""
 "C" "N" 470.300000 1.350000 ""
 "H" "N" 434.100000 1.010000 ""
 "C" "HA" 354.500000 1.080000 ""
!entry.e.parm.torsionOrders array str
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
 "0123"
!entry.e.parm.torsions table str type1 str type2 str type3 str type4
int type dbl kp int n dbl p0 str desc
 "CT" "N*" "CA" "H4" 0 0.300000 2 3.141594 ""
 "CC" "CA" "N*" "CT" 0 0.300000 2 3.141594 ""
 "CT" "N*" "CK" "H5" 0 0.300000 2 3.141594 ""
 "CT" "N*" "CK" "NB" 0 0.300000 2 3.141594 ""
 "CA" "N*" "CT" "H1" 0 0.0 2 0.0 ""
 "CK" "N*" "CT" "H1" 0 0.0 2 0.0 ""
 "N*" "CA" "CC" "NB" 0 3.625000 2 3.141594 ""
 "CT" "CC" "CA" "N*" 0 3.625000 2 3.141594 ""
 "CC" "NB" "CK" "N*" 0 0.0 3 3.141594 ""
 "CA" "N*" "CK" "H5" 0 0.300000 2 3.141594 ""
 "CA" "N*" "CK" "NB" 0 0.300000 2 3.141594 ""
 "CA" "CC" "NB" "CK" 0 0.0 3 3.141594 ""
 "CA" "CC" "CT" "HC" 0 0.0 2 0.0 ""
 "CA" "CC" "CT" "CT" 0 0.0 2 0.0 ""
 "CK" "N*" "CA" "H4" 0 0.300000 2 3.141594 ""
 "H4" "CA" "CC" "NB" 0 3.625000 2 3.141594 ""
 "CT" "CC" "CA" "H4" 0 3.625000 2 3.141594 ""
 "CC" "CA" "N*" "CK" 0 0.300000 2 3.141594 ""
 "CK" "NB" "CC" "CT" 0 0.0 3 3.141594 ""
 "CC" "NB" "CK" "H5" 0 0.0 3 3.141594 ""
 "HC" "CT" "CC" "NB" 0 0.0 2 0.0 ""
 "CT" "CT" "CC" "NB" 0 0.0 2 0.0 ""
 "C" "CT" "CT" "CC" 0 0.156000 3 0.0 ""
 "CC" "CT" "CT" "H1" 0 0.156000 3 0.0 ""
 "CC" "CT" "CT" "N" 0 0.156000 3 0.0 ""
 "CT" "CT" "C" "O" 0 0.0 2 3.141594 ""
 "CT" "CT" "C" "N" 0 0.0 2 3.141594 ""
 "CT" "CT" "N" "H" 0 0.0 2 0.0 ""
 "C" "N" "CT" "CT" 0 0.0 2 0.0 ""
 "C" "CT" "CT" "HC" 0 0.156000 3 0.0 ""
 "H1" "CT" "CT" "HC" 0 0.156000 3 0.0 ""
 "HC" "CT" "CT" "N" 0 0.156000 3 0.0 ""
 "CT" "C" "N" "H" 0 2.500000 2 3.141594 ""
 "CT" "N" "C" "HA" 0 2.500000 2 3.141594 ""
 "CT" "N" "C" "O" 0 2.500000 2 3.141594 ""
 "C" "CT" "N" "H" 0 0.0 2 0.0 ""
 "C" "CT" "N" "C" 0 0.0 2 0.0 ""
 "H1" "CT" "C" "O" 0 0.0 2 3.141594 ""
 "N" "CT" "C" "O" 0 0.0 2 3.141594 ""
 "H" "N" "C" "O" 0 2.500000 2 3.141594 ""
 "H1" "CT" "C" "N" 0 0.0 2 3.141594 ""
 "N" "C" "CT" "N" 0 0.0 2 3.141594 ""
 "H" "N" "CT" "H1" 0 0.0 2 0.0 ""
 "C" "N" "CT" "H1" 0 0.0 2 0.0 ""
 "H" "N" "C" "HA" 0 2.500000 2 3.141594 ""
 "CA" "CK" "N*" "CT" 1 1.100000 2 3.141594 ""
 "CC" "H4" "CA" "N*" 1 1.100000 2 3.141594 ""
 "H5" "N*" "CK" "NB" 1 1.100000 2 3.141594 ""
 "CA" "CT" "CC" "NB" 1 1.100000 2 3.141594 ""
 "CT" "N" "C" "O" 1 1.100000 2 3.141594 ""
 "HA" "N" "C" "O" 1 1.100000 2 3.141594 ""


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